|
| Status |
Public on Feb 05, 2014 |
| Title |
B cell CTCF |
| Sample type |
SRA |
| |
|
| Source name |
splenic B cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody: CTCF
chip antibody manufacturer: Millipore
cell type: splenic B cells
strain: C57BL/6
cell surface markers: CD43-
cell isolation: B cells were purified from the spleens of 6-week old mice using a magnetic bead based CD43- B cell Isolation Kit (Miltenyi).
|
| 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 Genome Analyzer II |
| |
|
| 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 |
| E-mail(s) |
cdschar@emory.edu
|
| 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 |
GPL9250 |
| Series (1) |
| GSE44637 |
CTCF binding in B cells and Plasmablasts |
|
| Relations |
| SRA |
SRX245508 |
| BioSample |
SAMN01924812 |
