Comment[ArrayExpressAccession] E-GEOD-44637 MAGE-TAB Version 1.1 Public Release Date 2014-02-05 Investigation Title CTCF binding in B cells and Plasmablasts Comment[Submitted Name] CTCF binding in B cells and Plasmablasts Experiment Description The mammalian CCCTC-binding factor (CTCF) regulates gene expression through the formation of higher order chromatin structures. Recent evidence has implicated a role for CTCF in regulating gene expression in the human MHCII locus. To investigate the role of CTCF in murine MHCII gene expression we mapped CTCF binding sites in B cells (MHCII+ cells) and Plasmablasts which are differentiated B cells that have silenced MHCII gene expression. These observations lead to the identification of differential CTCF binding during differentiation in these cell types and suggest mechanims of MHCII gene regulation. Comparison of CTCF binding in B cells and Plasmablasts in mice using ChIP-seq 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 Scharer Scharer Boss Person First Name Chris C J Person Email cdschar@emory.edu Person Affiliation Emory University Person Phone 404-727-5959 Person Address Microbiology and Immunology, Emory University, 1510 Clifton Rd, Suite 3120, Atlanta, GA, USA Person Roles submitter Protocol Name P-GSE44637-2 P-GSE44637-1 Protocol Description Raw sequencing reads were mapped to the mm9 version of the mouse genome with Bowtie using the following options to ensure each read mapped to a unique location -m 1 -n 1 HOMER software (Heinz et al. Mol Cell, 38:576-589) using the default parameters was used to identify significantly enriched CTCF peaks over input control for B cells and Plasmablasts Genome_build: mm9 Supplementary_files_format_and_content: Wig files were generated using HOMER and represent reads per million. Bed files contain the genomic locations of significantly enriched peaks, a unique peak ID, and the peak score as determined by the HOMER analysis Chromatin immunoprecipitation (ChIP) assay was performed as previously described (Scharer et al. Cancer Research, 69:709-717). Briefly, the indicated cells were fixed in 1% formaldehyde for 10 minutes, nuclei isolated, and sonicated to an average chromatin fragment size of 200-400 bp. 30 μg chromatin was immunoprecipitated with anti-CTCF (Millipore) antibody or control IgG serum over night at 4 degrees. Antibody-chromatin complexes were captured with Protein A magnetic beads (Invitrogen), cross-links reversed, and DNA purified. Input fraction was isolated from the IgG supernatant prior to washing. Sequencing libraries were prepared using the ChIP-seq Library Preparation Kit (Illumina) according to the manufacturers instructions using 10 ng of ChIP or input control DNA. B cell samples were sequenced on a single lane of an Illumina Genome Analyzer II instrument. Plasmablast samples were sequenced on a single lane of an Illumina HiSeq 2000 instrument. Protocol Type normalization data transformation protocol nucleic acid library construction protocol Experimental Factor Name CELL SURFACE MARKERS CELL ISOLATION CELL TYPE CHIP ANTIBODY Experimental Factor Type cell surface markers cell isolation cell type chip antibody Comment[SecondaryAccession] GSE44637 Comment[GEOReleaseDate] 2014-02-05 Comment[ArrayExpressSubmissionDate] 2013-02-25 Comment[GEOLastUpdateDate] 2014-02-14 Comment[AEExperimentType] ChIP-seq Comment[SecondaryAccession] SRP018843 Comment[SequenceDataURI] http://www.ebi.ac.uk/ena/data/view/SRR764902-SRR764905 SDRF File E-GEOD-44637.sdrf.txt