{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Emily Warman"],"instrument_platform":["Illumina HiSeq 2000"],"study_type":["ChIP-seq"],"organism":["Escherichia coli str. K-12 substr. MG1655"],"species":["Escherichia coli str. K-12 substr. MG1655"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16394"],"description":["ChIP-seq data for Escherichia coli strain MG1655 and MG1655 hns::kan. The strains were grown in LB medium at 37 degrees to log phase and crosslinked with 1% (v/v) formaldehyde. After sonication, to lyse cells and fragment DNA, immunoprecipitations were done using anti-NusA and anti-Rho antibodies. Libraries were prepared using DNA remaining after immunoprecipitation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sample Collection - Bacterial strain MG1655 is a laboratory strain of Escherichia coli.","Library Construction - Libraries were prepared using immunoprecipited protein-DNA complexes immobilised with Protein A-sepharose. DNA fragments were then blunt ended, A-tailed and barcoded. This was done using an NEB quick blunting and ligation kit, the Klenow fragment (5’-3’ exo-, NEB) and NEXTflex ChIP-seq barcodes (Bioo Scientific). Following elution of complexes from the Protein-A sepharose, crosslinks were reversed and barcoded libraries were amplified by PCR. The number of PCR cycles was determined empirically for each library. After amplification, library concentration was quantified using Qubit analysis and real time PCR.","Growth Protocol - Cells were grown in liquid LB minimal medium at 37 degrees with shaking.","Sequencing - Equimolar library concentrations were pooled and sequenced using an Illumina MiSeq instrument.","Nucleic Acid Extraction - Immunoprecipitations were done as described by Haycocks et al. (PLoS Pathog. 2015. 11:e1004605) using Vibrio cholerae strain MG1655. After growing cells to midlog phase, crosslinking, and sonication, protein DNA complexes were immunoprecipitated using anti-NusA or anti-Rho."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Emily Warman"],"additional_accession":[]},"is_claimable":false,"name":"Chip-seq analysis of NusA and Rho binding in Escherichia coli with or without H-NS","description":"ChIP-seq data for Escherichia coli strain MG1655 and MG1655 hns::kan. The strains were grown in LB medium at 37 degrees to log phase and crosslinked with 1% (v/v) formaldehyde. After sonication, to lyse cells and fragment DNA, immunoprecipitations were done using anti-NusA and anti-Rho antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.","dates":{"release":"2026-05-20T00:00:00Z","modification":"2026-05-20T01:01:29.436Z","creation":"2025-12-16T13:54:40.761Z"},"accession":"E-MTAB-16394","cross_references":{"ENA":["ERP186626"],"EFO":["EFO_0002944","EFO_0004170","EFO_0003789","EFO_0002692","EFO_0005518","EFO_0004184"]}}