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Sample GSM1180110 Query DataSets for GSM1180110
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
Reanalyzed by GSE80797
BioSample SAMN02225390
SRA SRX317633

Supplementary file Size Download File type/resource
GSM1180110_r091112_l4_PCT4961_nd_RNASeq.wig.gz 3.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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