biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsDavid GraingerNextSeq 2000ChIP-seqVibrio choleraeVibrio choleraehttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14434The experiment contains ChIP-seq data for an rpoS- version of Vibrio cholerae strain A1552, or a derivative encoding rpoS-3xFLAG. In both cases, smooth colony variants were used. The strains were both grown at 37 degrees, in LB medium, to an OD600 of 2.0, and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.biostudies-arrayexpressNucleic Acid Extraction - Immunoprecipitations were done as described by Haycocks et al (PLoS Genet. 2019. 15, e1008362) using derivatives of Vibrio cholerae strain A1552 using anti-FLAG antibodies (Sigma).Growth Protocol - Cells were grown in liquid LB medium, at 37 degrees with shaking, to an OD600 of 2.0.Sample Collection - The Vibrio cholerae O1 El Tor strain A1552 was isolated in 1992 from a traveller from Peru.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. 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.Sequencing - Equimolar library concentrations were pooled and sequenced using an Illumina instrument.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesDavid GraingerfalseChIP-seq analysis of RpoS in Vibrio choleraeThe experiment contains ChIP-seq data for an rpoS- version of Vibrio cholerae strain A1552, or a derivative encoding rpoS-3xFLAG. In both cases, smooth colony variants were used. The strains were both grown at 37 degrees, in LB medium, to an OD600 of 2.0, and crosslinked with 1 % (v/v) formaldehyde. After sonication, to break open cells and fragment DNA, immunoprecipitations were done using anti-FLAG antibodies. Libraries were prepared using DNA remaining after immunoprecipitation.2025-09-09T00:00:00Z2025-09-10T00:01:45.326Z2024-09-09T16:00:54.731ZE-MTAB-14434ERP163974EFO_0002944EFO_0004170EFO_0003789EFO_0002692EFO_0005518EFO_0004184