RolandSchmucki roland.schmucki@roche.com F. Hoffmann - La Roche AG

Grenzacherstrase Basel 4058 Switzerland

GEO

USA

TobiasHeckel IngaClausen MarcoPrunotto SannahJensen Zoffmann Gene Expression Omnibus (GEO) GEO NCBI NLM NIH http://www.ncbi.nlm.nih.gov/geo geo@ncbi.nlm.nih.gov 2015-05-20 2015-05-20 2018-01-10 GPL20227 high-throughput sequencing virtual Escherichia coli BW25113 2018-02-05 2019-03-25 2019-03-25 GSM2978339 SRA 1 AZ-LolCDE Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 200 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978340 SRA 1 AZ-LolCDE Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 200 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978341 SRA 1 AZ-LolCDE Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 200 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978342 SRA 1 B-01 Escherichia coli BW25113 BW25113 Gram-negative bacteria new hit EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978343 SRA 1 B-01 Escherichia coli BW25113 BW25113 Gram-negative bacteria new hit EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978344 SRA 1 B-01 Escherichia coli BW25113 BW25113 Gram-negative bacteria new hit EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978345 SRA 1 Ceftriaxone Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978346 SRA 1 Ceftriaxone Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978347 SRA 1 Ceftriaxone Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978348 SRA 1 Chloramphenicol Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978349 SRA 1 Chloramphenicol Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978350 SRA 1 Chloramphenicol Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978351 SRA 1 Ciprofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978352 SRA 1 Ciprofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978353 SRA 1 Ciprofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978354 SRA 1 Clarithromycin Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978355 SRA 1 Clarithromycin Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978356 SRA 1 Clarithromycin Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978357 SRA 1 Colistin Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.13 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978358 SRA 1 Colistin Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.13 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978359 SRA 1 Colistin Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.13 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978360 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978361 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978362 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978363 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978364 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978365 SRA 1 DMSO Escherichia coli BW25113 BW25113 Gram-negative bacteria control EC90 of phenotype ~ 25 min - bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978366 SRA 1 Doxycycline Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 7.5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978367 SRA 1 Doxycycline Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 7.5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978368 SRA 1 Doxycycline Escherichia coli BW25113 BW25113 Gram-negative bacteria Protein synthesis EC90 of phenotype ~ 25 min 7.5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978369 SRA 1 Globomycin Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978370 SRA 1 Globomycin Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978371 SRA 1 Globomycin Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor / lipoprotein EC90 of phenotype ~ 25 min 25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978372 SRA 1 Levofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978373 SRA 1 Levofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978374 SRA 1 Levofloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 0.75 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978375 SRA 1 Mecillinam Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978376 SRA 1 Mecillinam Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978377 SRA 1 Mecillinam Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 5 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978378 SRA 1 Meropenem Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.78 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978379 SRA 1 Meropenem Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.78 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978380 SRA 1 Meropenem Escherichia coli BW25113 BW25113 Gram-negative bacteria cell wall synthesis inhibitor EC90 of phenotype ~ 25 min 0.78 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978381 SRA 1 Nitrofurantoin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA damage EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978382 SRA 1 Nitrofurantoin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA damage EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978383 SRA 1 Nitrofurantoin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA damage EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978384 SRA 1 Nitroxolin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 100 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978385 SRA 1 Nitroxolin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 100 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978386 SRA 1 Nitroxolin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 100 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978387 SRA 1 Norfloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978388 SRA 1 Norfloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978389 SRA 1 Norfloxacin Escherichia coli BW25113 BW25113 Gram-negative bacteria DNA replication inhibitor EC90 of phenotype ~ 25 min 1 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978390 SRA 1 PolymyxineB Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978391 SRA 1 PolymyxineB Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978392 SRA 1 PolymyxineB Escherichia coli BW25113 BW25113 Gram-negative bacteria Membrane perturbation EC90 of phenotype ~ 25 min 0.25 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978393 SRA 1 Trimethoprim Escherichia coli BW25113 BW25113 Gram-negative bacteria Folic Acid synthesis inhibitor EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978394 SRA 1 Trimethoprim Escherichia coli BW25113 BW25113 Gram-negative bacteria Folic Acid synthesis inhibitor EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-25 GSM2978395 SRA 1 Trimethoprim Escherichia coli BW25113 BW25113 Gram-negative bacteria Folic Acid synthesis inhibitor EC90 of phenotype ~ 25 min 50 uM bacteria were treated with different antibiotics for ~ 25 min till ~OD 0.2 in 2 ml tubes bacteria were grown in iso-sensitest medium total RNA after treament bacteria were resuspended in QiaGen RNAprotect Bacteria Reagent (QiaGen #76506), incubated for 5min, centrifuged, and flash frozen on dry ice. Total RNA was extracted by incubating bacteria in Enzymatic Lysis Buffer (lysozyme & proteinase K) for 5 min followed by addition of QiaGen RLT Lysis Buffer and RNA purification using the QiaGen RNeasy Mini kit combined with DNase treatment on a solid support (QiaGen #74104). RNA quality assessment and quantification was performed using microfluidic chip analysis on an Agilent 2100 bioanalyzer (Agilent Technologies). For RNA-sequencing library preparation, 1000 ng total RNA was used as input. First, bacterial ribosomal RNA was depleted using the Ribo-Zero Magnetic Kit Bacteria (Illumina #MRZB12424). After depletion, RNA was resuspended in TruSeq Total RNA Sample Prep Kit Fragmentation buffer (8.5 ul RNA and 8.5 buffer) and reversed transcribed into cDNA using random hexamer primer. Then cDNA was further processed for the construction of sequencing libraries according to the manufacturer's recommendations using the TruSeq Stranded mRNA Sample Prep Kit (Illimina #RS-122-2101). Sequencing was performed with the Illumina TruSeq SBS Kit v4-HS chemistry (Illumina #FC-401-4003) on an Illumina HiSeq2500 instrument with 50 cycles of 2x50 bp paired-end sequencing. Illumina CASAVA v1.8.2 software used for basecalling and fastq file generation Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) genome using bowtie2 Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library. Genome_build: Escherichia coli str. K-12 substr. MG1655, complete genome (GenBank: U00096) Supplementary_files_format_and_content: tab-delimited text files in GCT format include read counts of uniquely and fraction of multiple mapped reads (counts.gct.gz), and normalized counts RPKM (rpkms.gct.gz) values for each sample RNA-Seq transcriptomic cDNA Illumina HiSeq 2500 NONE 2018-02-05 2019-03-25 2019-03-27 GSE110137 30899034

RNA-seq based transcriptome profiling allows a detailed molecular analysis of the E.coli transcriptome (~4200 genes) after perturbation with different antibiotics. Transcriptome fingerprints enable the identification of gene and pathway level responses to treatment to derive a mechanistic understanding of antibiotics mode of action and to differentiate antibiotics. For this goal, treatment has to be performed in a short time period and with sublethal concentrations of the antibiotics. Sublethal concentrations were chosen based on the EC90 concentration of the antibiotic necessary to change the cellular morphology compared to control conditions. Conclusions: Our study represents the first detailed analysis of E.coli transcriptomes after treatment with different antibiotics, with biologic replicates, generated by RNA-seq technology. The experimental design and data analysis reported here should provide a framework for comparative investigations of expression profiles of known and novel antibiotics. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

mRNA profiles of E.coli treated with different antibiotics at sublethal concentration and measured by deep RNA-sequencing, in triplicate, using Illumina HiSeq2500 Expression profiling by high throughput sequencing ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110137/suppl/GSE110137_counts.gct.gz ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE110nnn/GSE110137/suppl/GSE110137_rpkms.gct.gz