|
| Status |
Public on Jul 04, 2013 |
| Title |
mouse/plasmacytoma PCT4961/H3K4me3/rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse plasmacytoma PCT4961
|
| Organism |
Mus musculus |
| Characteristics |
antibody: H3K4me3
cell type: plasmacytoma PCT4961
strain: Balb/c
genotype: AID-/- BclXL
|
| 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-H3K4me3 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 |
SAMN02225380 |
| SRA |
SRX317622 |
