|
| Status |
Public on Jul 04, 2013 |
| Title |
mouse/in vitro activated B cell/H2BK5Ac/rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse, in vitro activated B cells
|
| Organism |
Mus musculus |
| Characteristics |
antibody: H2BK5Ac
cell type: in vitro activated B cells
strain: C57BL/6
|
| Growth protocol |
CD43− B cells were isolated from spleens by immunomagnetic depletion (Miltenyi Biotech). Purified cells were then activated in RPMI-1640 media with 10% (vol/vol) FCS, 1×antibiotic-antimycotic, 1% (wt/vol) glutamine, 1× non-essential amino acids, 1% (wt/vol) sodium pyruvate, 53uM 2-beta-mercapto-ethanol, and 10 mM Hepes for 72 h in the presence of 50ug/mL of LPS (Escherichia coli 0111:B4; Sigma) and 2.5 ng/mL of IL-4 (Sigma).
|
| 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-H2BK5Ac antibody following standard protocols. Immunoprecipitates were processed according to Illumina's standard protocol
|
| |
|
| 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 settings of GAPipeline using PhiX control; ***Raw data***: Fastq files contain full length reads that passed the chastity filter. Qualities were scaled to phred33 format for all files. ***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 (bowtie 0.12.8, --best --all --strata -m1 -n2 -l50). Redundancy was capped at a maximum of 3 identically aligned reads, and reads shifted by half the approximate fragment size of 120 towards the fragment center were counted in 100 nt bins along the genome. Counts were normalized to the non redundant library size and bin size such that the final units are reads per kb per million (RPKM).
|
| |
|
| Submission date |
Jul 03, 2013 |
| 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) |
| GSE48514 |
A mouse model of endemic Burkitt translocations reveals the long-range boundaries of Ig-mediated oncogene deregulation |
|
| Relations |
| BioSample |
SAMN02225391 |
| SRA |
SRX317620 |
