|
| Status |
Public on Feb 04, 2013 |
| Title |
HU_WT_Brdu_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Splenic B Cells
|
| Organism |
Mus musculus |
| Characteristics |
ChIP: Brdu
cell type: In vitro activated B Cells
strain: 129/Sv x C57BL/6
genotype: wildtype
growth duration: 28 hr
chip antibody: GE Healthcare, RPN-202 and BD Biosciences, 347580
treatment protocol: 10 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) in media containing 10 mcM BrdU for 28 hrs.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Illumina sequencing libraries were constructed from the random-primed BrdU-DNA material according to standard procedures according to Hansen et al. PNAS, 107, 139-144, 2010. Each library was 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 |
SRX217130 |
| BioSample |
SAMN01886662 |
