<?xml version="1.0" encoding="UTF-8"?>

<gse xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:noNamespaceSchemaLocation="esquema-gcs.xsd">

^DATABASE = GeoMiame
!Database_name = Gene Expression Omnibus (GEO)
!Database_institute = NCBI NLM NIH
!Database_web_link = http://www.ncbi.nlm.nih.gov/geo
!Database_email = geo@ncbi.nlm.nih.gov
^SERIES = GSE65711
!Series_title = Genome-wide OxyR and SoxRS transcriptional regulatory networks coordinate complex cellular responses to oxidative stress [RNA-seq]
!Series_geo_accession = GSE65711
!Series_status = Public on Aug 13 2015
!Series_submission_date = Feb 06 2015
!Series_last_update_date = Nov 16 2015
!Series_pubmed_id = 26279566
!Series_summary = Oxidative stress that originates from reactive oxygen species (ROS) is an inevitable consequence of aerobic respiration in bacteria. Three transcription factors (TFs), OxyR, SoxR, and SoxS play a critical role in transcriptional regulation of the defense system. However, the full genome-wide regulatory potential of them remains elusive. Here, we comprehensively reconstruct genome-wide OxyR, SoxR, and SoxS transcriptional regulatory networks in Escherichia coli under oxidative stress. Integrative data analysis reveals that OxyR, SoxR, and SoxS regulons are comprised of 38 genes in 28 transcription units (TUs), 11 genes in 10 TUs, and 34 genes in 25 TUs, respectively, significantly expanding the current knowledge of their regulatory networks. Comparison of them to other stress-response regulatory networks highlights minimal overlap between their regulons, indicating that E. coli has a series of relatively distinct stress responses covering the range of different stresses. We also demonstrate that these intricate networks coordinate detoxification process with DNA and protein damage repair, cell wall synthesis, divalent metal ion homeostasis, as well as metabolic robustness to produce overall response of E. coli to oxidative stress.
!Series_overall_design = A total of eight samples were analyzed. WT, ΔoxyR, ΔsoxR, and ΔsoxS  mutant cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Sang,W,Seo
!Series_contributor = Donghyuk,,Kim
!Series_sample_id = GSM1603386
!Series_sample_id = GSM1603387
!Series_sample_id = GSM1603388
!Series_sample_id = GSM1603389
!Series_sample_id = GSM1603390
!Series_sample_id = GSM1603391
!Series_sample_id = GSM1603392
!Series_sample_id = GSM1603393
!Series_contact_name = Donghyuk,,Kim
!Series_contact_email = donghyuk.kim@khu.ac.kr
!Series_contact_laboratory = Systems Biology Lab
!Series_contact_department = Department of Genetic Engineering
!Series_contact_institute = Kyung Hee University
!Series_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Series_contact_city = Yongin-si
!Series_contact_state = Gyeonggi-do
!Series_contact_zip/postal_code = 17104
!Series_contact_country = South Korea
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE65nnn/GSE65711/suppl/GSE65711_rnaseq_processed.csv.gz
!Series_platform_id = GPL16085
!Series_platform_taxid = 562
!Series_sample_taxid = 562
!Series_relation = SubSeries of: GSE65712
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA275132
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP053438
^PLATFORM = GPL16085
!Platform_title = Illumina MiSeq (Escherichia coli)
!Platform_geo_accession = GPL16085
!Platform_status = Public on Sep 20 2012
!Platform_submission_date = Sep 20 2012
!Platform_last_update_date = Sep 20 2012
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Escherichia coli
!Platform_taxid = 562
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM1603386
!Sample_title = <Name>WT PQ 1</Name>
!Sample_geo_accession = GSM1603386
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339605
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871628
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603387
!Sample_title = <Name>WT PQ 2</Name>
!Sample_geo_accession = GSM1603387
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>WT</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339610
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871629
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603388
!Sample_title = <Name>ΔoxyR PQ 1</Name>
!Sample_geo_accession = GSM1603388
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔoxyR PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-oxyR</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339609
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871630
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603389
!Sample_title = <Name>ΔoxyR PQ 2</Name>
!Sample_geo_accession = GSM1603389
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔoxyR PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-oxyR</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339608
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871631
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603390
!Sample_title = <Name>ΔsoxR PQ 1</Name>
!Sample_geo_accession = GSM1603390
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔsoxR PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-soxR</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339601
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871632
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603391
!Sample_title = <Name>ΔsoxR PQ 2</Name>
!Sample_geo_accession = GSM1603391
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔsoxR PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-soxR</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339602
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871633
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603392
!Sample_title = <Name>ΔsoxS PQ 1</Name>
!Sample_geo_accession = GSM1603392
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔsoxS PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-soxS</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339603
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871634
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0
^SAMPLE = GSM1603393
!Sample_title = <Name>ΔsoxS PQ 2</Name>
!Sample_geo_accession = GSM1603393
!Sample_status = Public on Aug 13 2015
!Sample_submission_date = Feb 06 2015
!Sample_last_update_date = Aug 13 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔsoxS PQ
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn>
!Sample_taxid_ch1 = 562
!Sample_characteristics_ch1 = strain: <Orgn>K-12 MG1655</Orgn>
!Sample_characteristics_ch1 = genotype/variation: <Gtype>delta-soxS</Gtype>
!Sample_characteristics_ch1 = treated with: <Supp>250 uM of paraquat</Supp> at <Phase>mid-log pahse</Phase> for <Supp>20 min</Supp>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, ΔoxyR, ΔsoxR, and ΔsoxS were grown to mid-log phase <Air>aerobically</Air> at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp>. Then cells were treated with 250 uM of paraquat at mid-log pahse for 20 min with agitation.
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was extracted using the RNeasy Plus Mini kit (Qiagen Inc., Valencia, CA, USA) and genomic DNA was removed by gDNA Eliminator spin column in the RNeasy Plus Mini Kit. RNA quality and concentration was determined by analysis with a NanoDrop 1000 (Thermo Scientific Inc., Wilmington, DE, USA).
!Sample_extract_protocol_ch1 = RNA libraries were prepared for sequencing using standard Illumina protocols
!Sample_data_processing = Sequenced reads were mapped onto NC_000913 reference genome sequence using bowtie v1.0.0 with parameters -X 1000 -n 2 -3 3 -S
!Sample_data_processing = Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using cufflinks v.1.3.0
!Sample_data_processing = Genome_build: <Gversion>NC_000913</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: comma-delimited text files include FPKM values for each Sample.
!Sample_platform_id = GPL16085
!Sample_contact_name = Donghyuk,,Kim
!Sample_contact_email = donghyuk.kim@khu.ac.kr
!Sample_contact_laboratory = Systems Biology Lab
!Sample_contact_department = Department of Genetic Engineering
!Sample_contact_institute = Kyung Hee University
!Sample_contact_address = 1732 Deokyoung-daero, Giheung-gu
!Sample_contact_city = Yongin-si
!Sample_contact_state = Gyeonggi-do
!Sample_contact_zip/postal_code = 17104
!Sample_contact_country = South Korea
!Sample_instrument_model = Illumina MiSeq
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = <Technique>RNA-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN03339604
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX871635
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE65711
!Sample_series_id = GSE65712
!Sample_data_row_count = 0

</gse>