|
| Status |
Public on Oct 18, 2018 |
| Title |
CD4 XBP1 wild type, replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: WT
replicate: 2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Tumor infiltrating CD4+ T cells sorted from peritoneal wash samples of Xbp1f/f (WT) or Xbp1f/f Cd4cre (KO) female mice bearing aggressive ID8-Defb29/Vegf-A ovarian cancer for 20 days. miRVana miRNA isolation kit (Ambion) and RNeasy MinElute kit (Qiagen) were used for total RNA isolation and concentration
Library preparation was performed using the UltraLowRNAseq RNA Library Prep Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
CD45+CD3+CD4+ peritoneal wash samples of Xbp1f/f mice
WT_CD4_2
|
| Data processing |
Reads produced from 51bp single end sequencing runs were aligned against mouse genome (mm9) using Bowtie v0.12.8 algorithm. Mouse mm9 transcriptome information was obtained from UCSC Genome Browser and the RSEM algorithm was used to calculate number of aligned tags for each gene
Differential expression between two groups were tested by EdgeR
Genome_build: mm9
Supplementary_files_format_and_content: Prosessed files contains the raw counts for each gene
|
| |
|
| Submission date |
Aug 10, 2018 |
| Last update date |
Oct 18, 2018 |
| Contact name |
Priyankara J Wickramasinghe |
| E-mail(s) |
priyaw@wistar.org
|
| Phone |
2154956837
|
| Organization name |
The Wistar Institute
|
| Department |
Bioinformatics
|
| Lab |
Genomics
|
| Street address |
3601 Spruce Street
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE118430 |
IRE1α-XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity |
|
| Relations |
| BioSample |
SAMN09809276 |
| SRA |
SRX4546383 |
