|
| Status |
Public on Mar 02, 2021 |
| Title |
EGR2 KO replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
Sorted LCMV-specific CD8+ T cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: LCMV H-2Kb GP33-41-specific CD8+ T cell
genotype: CD4-cre+ Egr2 flox/flox
background: C57BL/6J
|
| Treatment protocol |
CD4 depleted WT or cKO mice were infected with 2x10^6 pfu LCMV-Cl13 i.v.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At day 20 p.i., CD8+CD44int-hi H-2DbGP33-41-tetramer stained cells were isolated by fluorescence activated cell sorting. Total RNA was isolated using Trizol LS (Thermo Fisher Scientific) according to manufacturer’s instructions
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
normalizedERG2countslimmavoom.csv
|
| Data processing |
Reads were aligned to the mouse genome reference (GRCm38/mm10) sequence using HiSat2 (Kim et al., 2015) with default parameters.
Read counts were then generated for each gene in each sample using FeatureCounts from the Subread package (v1.5.0-p3).
|
| |
|
| Submission date |
Jul 22, 2019 |
| Last update date |
Mar 02, 2021 |
| Contact name |
Ian Parish |
| Organization name |
Peter MacCallum Cancer Centre
|
| Street address |
305 Grattan Street
|
| City |
Melbourne |
| State/province |
VIC |
| ZIP/Postal code |
3000 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE134689 |
Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance [RNA-seq I] |
| GSE134710 |
Antigen-driven EGR2 expression is required for exhausted CD8+ T cell stability and maintenance |
|
| Relations |
| BioSample |
SAMN12342271 |
| SRA |
SRX6491110 |
