 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Apr 19, 2016 |
| Title |
CD5hi_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Splenocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell phenotype: CD8+; CD44lo/CD49dlo; 20% highest expressers of CD5
strain: C57/Bl6
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy plus kit (Cat# 74134) in accordance with the supplied manual.
A modified Kapa Biosystems (Wilmington, MA, USA) KAPA Stranded mRNA-Seq kit for whole transcriptome libraries was used to primarily target all polyA RNA. Briefly, library construction proceeded from isolation of total RNA species, followed by mRNA (poly-A) isolation, 1st and 2nd strand cDNA synthesis, Life Technologies Ion adaptor ligation, amplification, and bead templating.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Sequence reads of 30 or more nt were mapped to the mm10 (GRCm38) assembly of the mouse genome with the STAR RNA-Seq aligner version 2.4.1d using gene annotation data from Ensembl version 78
For each gene in the Ensembl 78 annotation, reads were counted using the HTSeq software version 0.6.0
Statistical comparisons of the gene expression between the cell types were performed with the DESeq2 package version 1.8.1 for the R statistical software version 3.2.0.
Genome_build: mm10
|
| |
|
| Submission date |
Feb 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ross M. Kedl |
| E-mail(s) |
ross.kedl@ucdenver.edu, ross.kedl@cuanschutz.edu
|
| Phone |
303-724-8671
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Immunology and Microbiology
|
| Street address |
12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE78247 |
Analysis of gene-expression in normal, unmanipulated naïve (CD44lo/CD49dlo; CD5lo/CD5hi) and Virtual memory (CD44hi/CD49dlo) T cells |
|
| Relations |
| BioSample |
SAMN04513208 |
| SRA |
SRX1598235 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
