|
| Status |
Public on Jul 04, 2013 |
| Title |
mouse/plasmacytoma PCT4961/RNASeq/rep1 |
| Sample type |
SRA |
| |
|
| Source name |
mouse plasmacytoma PCT4961
|
| Organism |
Mus musculus |
| Characteristics |
antibody: RNASeq
cell type: plasmacytoma PCT4961
strain: Balb/c
genotype: AID-/- BclXL
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated with Trizol and libraries were generated with TrueSeq kits according to manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
base calling and fastq file generation: Standard illumina pipeline tools; alignment: gsnap [--novelsplicing=0 --use-splicing=mm9.splices.iit --format=sam --batch=4] filtered to an alignment quality of 20 or more; wig file: Redundancy was capped at a maximum of 3 identically aligned reads and reads 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 |
| Reanalyzed by |
GSE80797 |
| BioSample |
SAMN02225390 |
| SRA |
SRX317633 |
