|
| Status |
Public on Jan 02, 2013 |
| Title |
activatedB_H2AXko_RPAip_a |
| Sample type |
SRA |
| |
|
| Source name |
in vitro activated B cells
|
| Organism |
Mus musculus |
| Characteristics |
chip antibody manufacturer: Calbiochem
chip antibody catalog #: NA19L
chip antibody lot #: multiple lots
cell type: in vitro activated B cells
strain: C57BL/6
genotype: H2AXko
chip antibody: RPA
|
| Growth protocol |
CD43- resting B cells were isolated from mouse spleens by negative selection with magnetic beads (Miltenyi Biotech). Following isolation, resting B cells were stimulated with LPS (50 mcg/ml) and IL-4 (2.5 ng/ml) for 72 hrs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% paraformaldehyde at 37C for 10 minutes followed by quenching with glycine and sonnication. Chromatin fragments were then immunoprecipitated with an anti-CTCF antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol and sequenced on a Genome Analyzer II or HiSeq2000.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Image analysis, base calling, quality filtering: Standard Illumina tools (different versions); ***Raw data***: Fastq files contain full length reads that passed the chastity filter. ***Wig file***: Reads were aligned to the mouse genome (build mm9) with bowtie accepting only reads that had a unique match in the genome in their top quality stratum. Redundancy was capped at 3 reads per position and shifted reads were counted in 400 nt bins across the genome. Counts were normalized to the reduced redundancy library size and bin size such that the final units are reads per kb per million (RPKM).
|
| |
|
| Submission date |
Nov 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Seolkyoung Jung |
| Organization name |
NIH
|
| Department |
NIAMS
|
| Lab |
biodata mining and discovery section
|
| Street address |
10 Center Dr
|
| City |
bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE42451 |
RPA accumulation during class switch recombination represents 5'-3' DNA end resection during the S-G2/M phase of the cell cycle |
|
| Relations |
| SRA |
SRX205952 |
| BioSample |
SAMN01818216 |
