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^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 = GSE74932
!Series_title = The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons [ChIP-seq]
!Series_geo_accession = GSE74932
!Series_status = Public on Dec 01 2015
!Series_submission_date = Nov 12 2015
!Series_last_update_date = Dec 17 2015
!Series_pubmed_id = 26670385
!Series_summary = As descirbed in the manuscript "The impact of anaerobiosis on expression of the iron-responsive Fur and RyhB Regulons" we mapped the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.
!Series_overall_design = We performed ChIP-Seq to map the locations of Fur DNA binding in E. coli K12 under aerobic or anaerobic growth conditions and anerobic iron deficient growth conditions.
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Nicole,A,Beauchene
!Series_contributor = Kevin,S,Myers
!Series_contributor = Dongjun,,Chung
!Series_contributor = Dan,M,Park
!Series_contributor = Allison,M,Weisnicht
!Series_contributor = Sunduz,,Keles
!Series_contributor = Patricia,J,Kiley
!Series_sample_id = GSM1937964
!Series_sample_id = GSM1937965
!Series_sample_id = GSM1937966
!Series_sample_id = GSM1937967
!Series_sample_id = GSM1937968
!Series_sample_id = GSM1937969
!Series_sample_id = GSM1937970
!Series_sample_id = GSM1937971
!Series_sample_id = GSM1937972
!Series_contact_name = Patricia,J,Kiley
!Series_contact_email = pjkiley@wisc.edu
!Series_contact_department = Biomolecular Chemistry
!Series_contact_institute = University of Wisconsin - Madison
!Series_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Series_contact_city = Madison
!Series_contact_state = WI
!Series_contact_zip/postal_code = 53706
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE74nnn/GSE74932/suppl/GSE74932_RAW.tar
!Series_platform_id = GPL15010
!Series_platform_id = GPL17024
!Series_platform_taxid = 511145
!Series_sample_taxid = 511145
!Series_relation = SubSeries of: GSE74933
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA301961
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP066093
^PLATFORM = GPL15010
!Platform_title = Illumina HiSeq 2000 (Escherichia coli str. K-12 substr. MG1655)
!Platform_geo_accession = GPL15010
!Platform_status = Public on Dec 14 2011
!Platform_submission_date = Dec 14 2011
!Platform_last_update_date = May 28 2014
!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
^PLATFORM = GPL17024
!Platform_title = Illumina Genome Analyzer IIx (Escherichia coli str. K-12 substr. MG1655)
!Platform_geo_accession = GPL17024
!Platform_status = Public on Apr 16 2013
!Platform_submission_date = Apr 16 2013
!Platform_last_update_date = Apr 16 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 = GSM1937964
!Sample_title = <Name>Fur IP ChIP-Seq Aerobic A</Name>
!Sample_geo_accession = GSM1937964
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Aerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL17024
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261714
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427675
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937964/suppl/GSM1937964_Fur_IP_ChIP_seq_Aerobic_A_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937965
!Sample_title = <Name>Fur IP ChIP-Seq Aerobic B</Name>
!Sample_geo_accession = GSM1937965
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Aerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261715
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427676
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937965/suppl/GSM1937965_Fur_IP_ChIP_seq_Aerobic_B_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937966
!Sample_title = <Name>Fur IP ChIP-Seq Aerobic C</Name>
!Sample_geo_accession = GSM1937966
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Aerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown <Air>aerobically (70% N2, 25% O2, and 5% CO2)</Air> or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261716
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427677
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937966/suppl/GSM1937966_Fur_IP_ChIP_seq_Aerobic_C_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937967
!Sample_title = <Name>Fur IP ChIP-Seq Anaerobic A</Name>
!Sample_geo_accession = GSM1937967
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Anaerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL17024
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina Genome Analyzer IIx
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261717
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427678
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937967/suppl/GSM1937967_Fur_IP_ChIP_seq_Anaerobic_A_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937968
!Sample_title = <Name>Fur IP ChIP-Seq Anaerobic B</Name>
!Sample_geo_accession = GSM1937968
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Anaerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261718
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427679
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937968/suppl/GSM1937968_Fur_IP_ChIP_seq_Anaerobic_B_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937969
!Sample_title = <Name>Fur IP ChIP-Seq Anaerobic C</Name>
!Sample_geo_accession = GSM1937969
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = <Air>Anaerobic</Air> cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Wild-type</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>10 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261719
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427680
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937969/suppl/GSM1937969_Fur_IP_ChIP_seq_Anaerobic_C_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937970
!Sample_title = <Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient A</Name>
!Sample_geo_accession = GSM1937970
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Anaerobic, Iron Deficient cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>{delta}lacZ, {delta}tonB, {delta}feoA, {delta}zupT K12</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261720
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427681
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937970/suppl/GSM1937970_Fur_IP_ChIP_seq_AnaerobicIronDef_A_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937971
!Sample_title = <Name>Fur IP ChIP-Seq Anaerobic, Iron Deficient B</Name>
!Sample_geo_accession = GSM1937971
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Anaerobic, Iron Deficient cultures
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>{delta}tonB, {delta}feoA, {delta}zupT K12</Gtype>
!Sample_characteristics_ch1 = growth medium: <Med>MOPS minimal glucose media</Med> containing <Supp>1 µM FeSO4</Supp>
!Sample_characteristics_ch1 = chip antibody: Custom <Anti>anti-Fur polyclonal antibody</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or <Air>anaerobically (95% N2 and 5% CO2)</Air> until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261721
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427682
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937971/suppl/GSM1937971_Fur_IP_ChIP_seq_AnaerobicIronDef_B_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0
^SAMPLE = GSM1937972
!Sample_title = <Name>Input ChIP-Seq</Name>
!Sample_geo_accession = GSM1937972
!Sample_status = Public on Dec 01 2015
!Sample_submission_date = Nov 12 2015
!Sample_last_update_date = Dec 01 2015
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Combined input
!Sample_organism_ch1 = <Orgn>Escherichia coli str. K-12 substr. MG1655</Orgn>
!Sample_taxid_ch1 = 511145
!Sample_characteristics_ch1 = genotype/variation: <Gtype>Combined input</Gtype>
!Sample_characteristics_ch1 = growth medium: Combined input
!Sample_characteristics_ch1 = chip antibody: <Anti>none</Anti>
!Sample_treatment_protocol_ch1 = <Supp>Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final)</Supp> was added to the <Phase>mid-log</Phase> cultures followed by formaldehyde to 1% final, and aerobic or anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with aerobic or anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 3500 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.
!Sample_treatment_protocol_ch1 = Custom anti-Fur antibodies were purified over a His6-Fur bound HiTrap NHS-activated HP column (GE Healthcare) as previously described (PMID: 21478858). Western blot analyses showed that the purified antibody was specific for Fur.
!Sample_growth_protocol_ch1 = Cells were grown aerobically (70% N2, 25% O2, and 5% CO2) or anaerobically (95% N2 and 5% CO2) until <Phase>mid-log phase</Phase> (<OD>OD600 of ~0.3-0.35</OD>).
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Cell pellets (from initial 250 mL of culture) were thawed and resuspended in 250 μL of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 1% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml), micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then precleared through incubation with a 50/50 slurry of sepharose protein A beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of sepharose protein A beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2% TritonX-100), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes to remove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50 μl with EB.
!Sample_extract_protocol_ch1 = DNA samples were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation. All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 50 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  For aerobic and anaerobic replicates A, a single read, 50 bp run was performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx. For aerobic and anaerobic replicates B and C, the input, and the anaerobic, iron deficient samples, a single read, 50 bp run was performed, using standard SBS kits (v3) and SCS 1.8.2 on an Illumina HiSeq2000.
!Sample_data_processing = Reformat Illumina files to Sanger format, FASTQ Groomer
!Sample_data_processing = Map reads to theEscherichia coli MG1655 K-12 genome, Bowtie 2
!Sample_data_processing = Call peaks to and FDR 0.1, MOSAiCs
!Sample_data_processing = Deconvolute peaks in close proximity, dPeak
!Sample_data_processing = Require peaks to be present in at least 2 replicates and conform to a peak shape by visual inspection
!Sample_data_processing = Scale data set to 20 million reads
!Sample_data_processing = Genome_build: Escherichia coli MG1655 K-12 genome version <Gversion>U00096.2</Gversion>
!Sample_data_processing = Supplementary_files_format_and_content: Processed data files contain the number of reads mapped to each base pair after the total number of reads were scaled to 20 million reads per experiment
!Sample_platform_id = GPL15010
!Sample_contact_name = Patricia,J,Kiley
!Sample_contact_email = pjkiley@wisc.edu
!Sample_contact_department = Biomolecular Chemistry
!Sample_contact_institute = University of Wisconsin - Madison
!Sample_contact_address = 420 Henry Mall, Room 1135 Biochemistry Building
!Sample_contact_city = Madison
!Sample_contact_state = WI
!Sample_contact_zip/postal_code = 53706
!Sample_contact_country = USA
!Sample_instrument_model = Illumina HiSeq 2000
!Sample_library_selection = ChIP
!Sample_library_source = genomic
!Sample_library_strategy = <Technique>ChIP-Seq</Technique>
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN04261722
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX1427683
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1937nnn/GSM1937972/suppl/GSM1937972_Input_ChIP_seq_WIG.wig.gz
!Sample_series_id = GSE74932
!Sample_series_id = GSE74933
!Sample_data_row_count = 0

</gse>