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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 05, 2014 |
| Title |
Plasmablast CTCF |
| Sample type |
SRA |
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| Source name |
splenic Plasmablasts
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| Organism |
Mus musculus |
| Characteristics |
chip antibody: CTCF
chip antibody manufacturer: Millipore
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.
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| 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Feb 25, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Chris Scharer |
| E-mail(s) |
cdschar@emory.edu
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| Organization name |
Emory University
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| Department |
Microbiology and Immunology
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| Lab |
Chris Scharer
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| Street address |
1510 Clifton Rd, Suite 3086A
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| City |
Atlanta |
| State/province |
GA |
| ZIP/Postal code |
30322 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE44637 |
CTCF binding in B cells and Plasmablasts |
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| Relations |
| SRA |
SRX245510 |
| BioSample |
SAMN01924814 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1088171_Plasmablast.CTCF.ChIPseq.bedgraph.gz |
95.6 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM1088171_Plasmablast.CTCF.peaks.txt.gz |
406.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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