|
| Status |
Public on Feb 04, 2013 |
| Title |
NT_53BP1pp_Smc5 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic B Cells
|
| Organism |
Mus musculus |
| Characteristics |
ChIP: Smc5
cell type: In vitro activated B Cells
strain: 129/Sv x C57BL/6
genotype: wildtype
growth duration: 72 hr
chip antibody: Calbiochem, DR1030
treatment protocol: 0 mM hydroxyurea for 6 hrs
|
| 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 (25 mcg/ml, Sigma) and IL-4 (5 ng/ml, Sigma) for 72 hrs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% paraformaldehyde followed by quenching with 0.125 glycine and sonication. Chromatin fragments were then immunoprecipitated with the antibodies shown in the sample characteristics following protocols described in the manuscript. Immunoprecipitates were processed following Illumina’s protocol and sequenced on a Genome Analyzer IIx.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Illumina Casava1.7.0 or 1.8.0 software used for basecalling.
Sequenced reads were trimmed, and masked for low-quality sequence, then mapped to mm9 whole genome using bowtie v0.12.8 determined uniquely aligned reads with at most 2 mismatches.
SICER with parameters: e-value, 100, gap size 600 (200) for RPA and γ−H2AX (BRCA1 and SMC5) is used to find enriched bins over Poisson distribution. Then the enrichment of bins passing the first criterion was examined relative to whole-cell extract control based on FDR of 1x10-5. Subsequently, the identified enriched windows that were less than 5 kbp apart were merged to delineate islands.
Genome_build: mm9
|
| |
|
| Submission date |
Jan 15, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Robert Babak Faryabi |
| E-mail(s) |
faryabi@pennmedicine.upenn.edu
|
| Phone |
215-573-8220
|
| Organization name |
University of Pennsylvania
|
| Department |
Pathology
|
| Lab |
Faryabi Lab
|
| Street address |
Room 553 BRB II/III, 421 Curie Boulevard
|
| City |
Philadelphia |
| State/province |
Pennsylvania |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE43504 |
Genome-wide mapping of early replication fragile sites (ERFS) |
|
| Relations |
| SRA |
SRX217128 |
| BioSample |
SAMN01886660 |
