|
| Status |
Public on Apr 24, 2014 |
| Title |
xbp1 fl/+ cells transduced with p210-neo and ERT2-Cre, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
BCR-ABL1 transformed murine ALL-like cells, Xbp1 heterozygous deletion
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BCR-ABL1 transformed murine ALL-like cells
genetic background: C57BL/6
genotype: Xbp1 heterozygous deletion
|
| Growth protocol |
The murine p210 transduced murine Xbp1 fl/+ pre-B cells Xbp1 were maintained in Iscove’s modified Dulbecco’s medium (IMDM, Invitrogen) with GlutaMAX containing 20% fetal bovine serum, 100 IU ml−1 penicillin, 100 μg ml−1 streptomycin and 50 µM 2-mercaptoethanol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Libraries were prepared according to a version of Illumina's mRNA-Seq protocol (Illumina, CA)
Libraries were prepared using the Illumina RNA-seq Library preparation Kit following the manufacture’s instructions (Illumina, CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
mRNA isolated from mouse Xbp1 heterozygous deletion cells
|
| Data processing |
Raw image data were converted into base calls and fastq files via the Illumina pipeline CASAVA version 1.8 with default parameters. All 50-bp-long reads were mapped to the reference mouse genome sequence, mm9, using Tophat aligner (Trapnell et al, Bioinformatics 2009, 25 (9): 1105-1111) with the default parameters. The mRNA expression level for each gene was represented as log2 RPKM (reads per kilobase per million reads), called by Seqgene (Deng et al, BMC Bioinformatics 2011, 12:267).
Genome_build: mm9
Supplementary_files_format_and_content: normalized abundance measurements log2 RPKM for the 6 samples
|
| |
|
| Submission date |
Dec 27, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Huimin Geng |
| E-mail(s) |
huimin.geng@ucsf.edu
|
| Organization name |
UCSF
|
| Department |
Department of Laboratory Medicine
|
| Street address |
513 Parnassus Ave., MSB S-1480
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE53683 |
A mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia [HTS] |
| GSE53685 |
A mechanistic rationale for targeting the unfolded protein response in pre-B acute lymphoblastic leukemia |
|
| Relations |
| BioSample |
SAMN02486622 |
| SRA |
SRX399644 |
