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Sample GSM1088172 Query DataSets for GSM1088172
Status Public on Feb 05, 2014
Title Plasmablast Input
Sample type SRA
Source name splenic Plasmablasts
Organism Mus musculus
Characteristics chip antibody: none
cell type: splenic Plasmablasts
strain: C57BL/6
cell surface markers: CD138+
cell isolation: Plasmablasts were induced by injecting 6-week old mice with 50 ug LPS retro-orbitally. 3 days post-injection spleens were harvested and plasmablasts purified by flow cytometry based on surface expression of CD138.
Extracted molecule genomic DNA
Extraction protocol 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.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing 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
Submission date Feb 25, 2013
Last update date May 15, 2019
Contact name Chris Scharer
Organization name Emory University
Department Microbiology and Immunology
Lab Chris Scharer
Street address 1510 Clifton Rd, Suite 3086A
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
Platform ID GPL13112
Series (1)
GSE44637 CTCF binding in B cells and Plasmablasts
SRA SRX245511
BioSample SAMN01924815

Supplementary file Size Download File type/resource
GSM1088172_Plasmablast.Input.ChIPseq.bedgraph.gz 97.8 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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