Comment[ArrayExpressAccession] E-GEOD-46414 MAGE-TAB Version 1.1 Public Release Date 2013-10-17 Investigation Title The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli [ChIP-Seq] Comment[Submitted Name] The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli [ChIP-Seq] Experiment Description We found many binding sites for ArcA under glucose fermentative anaerobic growth conditions. Descirbed in the manuscript "The response regulator ArcA uses a diverse binding site architechture to globally regulate carbon oxidation in E. coli" Examination of occupancy of ArcA under anaerobic growth conditions. Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Park Park Acktar Ansari Landick Kiley Person First Name Dan Dan Sohail Aseem Robert Patricia Person Email danmpark85@gmail.com Person Affiliation UW Madison Person Address UW Madison, 440 Henry Mall, Madison, WI, USA Person Roles submitter Protocol Name P-GSE46414-5 P-GSE46414-4 P-GSE46414-1 P-GSE46414-3 P-GSE46414-2 Protocol Description Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches. Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files). For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads. genome build: U00096.2 Genome Build: ArcA_anaerobic_ChIP-seq_IP_B.wig: U00096.2 Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches. Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files). For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads. genome build: U00096.2 Genome Build: ArcA_anaerobic_ChIP-seq_IP_A.wig: U00096.2 Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% 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 M-0C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 M-NM-4 hr. 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 incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 M-0C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 M-NM-