<?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 = GSE66481
!Series_title = Decoding genome-wide GadEWX transcriptional regulatory networks reveals a multifaceted cellular response to acid stress in Escherichia coli [RNA-seq]
!Series_geo_accession = GSE66481
!Series_status = Public on Aug 11 2015
!Series_submission_date = Mar 03 2015
!Series_last_update_date = Aug 12 2015
!Series_pubmed_id = 26258987
!Series_summary = The response to acid stress is a fundamental process in bacteria. Three transcription factors, GadE, GadW, and GadX (GadEWX) are known to play a critical role in the transcriptional regulation of glutamate-dependent acid resistance (GDAR) system in Escherichia coli K-12 MG1655. However, the regulatory role of GadEWX in coordinating interacting cellular functions is still unknown. Here, we comprehensively reconstruct genome-wide GadEWX transcriptional regulatory network in E. coli K-12 MG1655 under acidic stress. Integrative data analysis reveals that GadEWX regulons are comprised of 45 genes in 31 transcription units (TUs), significantly expanding the current knowledge of the GadEWX regulatory network. We demonstrate that GadEWX directly and coherently regulate several proton efflux/influx and generating/consuming enzymes with pairs of negative-feedback loops to maintain pH homeostasis by controlling proton flow. In addition, GadEWX regulate genes with assorted functions including molecular chaperones, acid resistance, stress response, and other regulatory activities. These results present a comprehensive understating on how GadEWX simultaneously coordinates many other cellular processes to produce the overall response of E. coli to acid stress.
!Series_overall_design = A total of eight samples were analyzed. WT and gadEWX mutant cells were cultured in M9 glucose minimal media at pH 5.5 with biological duplicates.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Sang,W,Seo
!Series_contributor = Donghyuk,,Kim
!Series_sample_id = GSM1623160
!Series_sample_id = GSM1623161
!Series_sample_id = GSM1623162
!Series_sample_id = GSM1623163
!Series_sample_id = GSM1623164
!Series_sample_id = GSM1623165
!Series_sample_id = GSM1623166
!Series_sample_id = GSM1623167
!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/GSE66nnn/GSE66481/suppl/GSE66481_rnaseq_processed.csv.gz
!Series_platform_id = GPL16085
!Series_platform_taxid = 562
!Series_sample_taxid = 562
!Series_relation = SubSeries of: GSE66482
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA277048
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP055778
^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 = GSM1623160
!Sample_title = <Name>WT pH5.5 1</Name>
!Sample_geo_accession = GSM1623160
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT pH5.5
!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 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383857
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895926
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623161
!Sample_title = <Name>WT pH5.5 2</Name>
!Sample_geo_accession = GSM1623161
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 11 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = WT pH5.5
!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 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383859
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895927
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623162
!Sample_title = <Name>ΔgadE pH5.5 1</Name>
!Sample_geo_accession = GSM1623162
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadE pH5.5
!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-gadE</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383862
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895928
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623163
!Sample_title = <Name>ΔgadE pH5.5 2</Name>
!Sample_geo_accession = GSM1623163
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadE pH5.5
!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-gadE</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383861
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895929
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623164
!Sample_title = <Name>ΔgadW pH5.5 1</Name>
!Sample_geo_accession = GSM1623164
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadW pH5.5
!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-gadW</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383858
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895930
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623165
!Sample_title = <Name>ΔgadW pH5.5 2</Name>
!Sample_geo_accession = GSM1623165
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadW pH5.5
!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-gadW</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383864
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895931
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623166
!Sample_title = <Name>ΔgadX pH5.5 1</Name>
!Sample_geo_accession = GSM1623166
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadX pH5.5
!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-gadX</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383860
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895932
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0
^SAMPLE = GSM1623167
!Sample_title = <Name>ΔgadX pH5.5 2</Name>
!Sample_geo_accession = GSM1623167
!Sample_status = Public on Aug 11 2015
!Sample_submission_date = Mar 03 2015
!Sample_last_update_date = Aug 12 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = ΔgadX pH5.5
!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-gadX</Gtype>
!Sample_characteristics_ch1 = growth phase: <Phase>mid-log phase</Phase> (<OD>OD600 = 0.3</OD>)
!Sample_treatment_protocol_ch1 = The cell culture was treated with the RNAprotect reagent (Qiagen).
!Sample_growth_protocol_ch1 = E. coli K-12 MG1655 WT, gadE, gadW and gadX mutant cells were grown to mid-log phase (OD600 = 0.3) <Air>aerobically</Air> (<Agit>250 rpm</Agit>) at <Temp>37°C</Temp> in <Med>M9 minimal media</Med> supplemented with <Supp>0.2% glucose</Supp> at <pH>pH 5.5</pH>.
!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/SAMN03383863
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX895933
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE66481
!Sample_series_id = GSE66482
!Sample_data_row_count = 0

</gse>