<?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 = GSE88980
!Series_title = Revealing the genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles and unexpected importance of narU under osmotic stress in Escherichia coli K-12 MG1655 [RNA-seq]
!Series_geo_accession = GSE88980
!Series_status = Public on Jun 09 2017
!Series_submission_date = Oct 20 2016
!Series_last_update_date = Jun 09 2017
!Series_pubmed_id = 28526842
!Series_summary = A transcription factor (TF), OmpR, plays a critical role in transcriptional regulation of the defense system for osmotic stress in bacteria. However, its full genome-wide regulatory potential is unknown. Here, we perform a genome-scale reconstruction of the OmpR regulon in Escherichia coli K-12 MG1655. Integrative data analysis reveals that a total of 37 genes in 24 transcription units (TUs) belong to OmpR regulon. Among them, 26 genes show more than two-fold changes in expression level under OmpR knock-out condition. We find that OmpR tends to regulate mostly membrane-located gene products of diverse fundamental biological processes, such as narU, ompX, and nuoN. Investigating co-regulation of entire set of genes regulated by other stress-response TFs unveils that they are surprisingly independently regulated by TF(s) responding to each stress. Additionally, detailed investigation of physiological roles of newly discovered OmpR regulon reveals that activation of narU encoding nitrate/nitrite transporter is a relatively unique strategy of E. coli K-12 MG1655 to significantly improve cellular tolerance toward osmotic stress.
!Series_overall_design = A total of four samples were analyzed. WT and ΔompR  mutant cells were cultured in M9 minimal media with 0.2% glucose. Then cells were treated with 0.3 M of NaCl at mid-log pahse for 30 min with agitation.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Sang-Woo,,Seo
!Series_contributor = Donghyuk,,Kim
!Series_sample_id = GSM2356687
!Series_sample_id = GSM2356688
!Series_sample_id = GSM2356689
!Series_sample_id = GSM2356690
!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/GSE88nnn/GSE88980/suppl/GSE88980_rnaseq_processed.csv.gz
!Series_platform_id = GPL17439
!Series_platform_taxid = 511145
!Series_sample_taxid = 511145
!Series_relation = SubSeries of: GSE88981
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA349458
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP091860
^PLATFORM = GPL17439
!Platform_title = Illumina MiSeq (Escherichia coli str. K-12 substr. MG1655)
!Platform_geo_accession = GPL17439
!Platform_status = Public on Jul 12 2013
!Platform_submission_date = Jul 12 2013
!Platform_last_update_date = Jul 12 2013
!Platform_technology = high-throughput sequencing
!Platform_distribution = virtual
!Platform_organism = Escherichia coli str. K-12 substr. MG1655
!Platform_taxid = 511145
!Platform_contact_name = ,,GEO
!Platform_contact_country = USA
!Platform_data_row_count = 0
^SAMPLE = GSM2356687
!Sample_title = <Name>WT NaCl 1</Name>
!Sample_geo_accession = GSM2356687
!Sample_status = Public on Jun 09 2017
!Sample_submission_date = Oct 20 2016
!Sample_last_update_date = Jun 09 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Total RNA isolated from E. coli
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>WT</Gtype>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</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 <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> 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 = GPL17439
!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/SAMN05930260
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2254712
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE88980
!Sample_series_id = GSE88981
!Sample_data_row_count = 0
^SAMPLE = GSM2356688
!Sample_title = <Name>WT NaCl 2</Name>
!Sample_geo_accession = GSM2356688
!Sample_status = Public on Jun 09 2017
!Sample_submission_date = Oct 20 2016
!Sample_last_update_date = Jun 09 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Total RNA isolated from E. coli
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>WT</Gtype>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</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 <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> 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 = GPL17439
!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/SAMN05930266
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2254713
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE88980
!Sample_series_id = GSE88981
!Sample_data_row_count = 0
^SAMPLE = GSM2356689
!Sample_title = <Name>ΔompR NaCl 1</Name>
!Sample_geo_accession = GSM2356689
!Sample_status = Public on Jun 09 2017
!Sample_submission_date = Oct 20 2016
!Sample_last_update_date = Jun 09 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Total RNA isolated from E. coli
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>ompR deletion mutant</Gtype>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</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 <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> 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 = GPL17439
!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/SAMN05930265
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2254714
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE88980
!Sample_series_id = GSE88981
!Sample_data_row_count = 0
^SAMPLE = GSM2356690
!Sample_title = <Name>ΔompR NaCl 2</Name>
!Sample_geo_accession = GSM2356690
!Sample_status = Public on Jun 09 2017
!Sample_submission_date = Oct 20 2016
!Sample_last_update_date = Jun 09 2017
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Total RNA isolated from E. coli
!Sample_organism_ch1 = <Orgn>Escherichia coli</Orgn> str. <Strain>K-12</Strain> substr. <Substrain>MG1655</Substrain>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = strain: K-12 MG1655
!Sample_characteristics_ch1 = genotype: <Gtype>ompR deletion mutant</Gtype>
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT and ΔompR were grown to <Phase>mid-log phase</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 <Supp>0.3 M of NaCl</Supp> at mid-log pahse for <Supp>30 min</Supp> 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 = GPL17439
!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/SAMN05930264
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX2254715
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE88980
!Sample_series_id = GSE88981
!Sample_data_row_count = 0

</gse>