|
| Status |
Public on Jun 13, 2023 |
| Title |
D8_Het_EEC_Rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Arid1a Het EEC cells, d8
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Arid1a Het
cell type: P14 CD8+
time: Day 8
infection: LCMV Armstrong
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy Plus Micro kit (Qiagen) and quantified with Agilent 4200 TapeStation.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA kit following manufacturer's protocols.
RNA-seq 51bp single-end sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
d8/bam/mm39/Het_EEC1_S18_R1_001.bam
featureCounts.d8.mm39.vM27.final.txt
|
| Data processing |
Sequence reads were aligned to GRCm39 (mm39) using STAR v2.5.3a (parameters- default)
RNA expression was quantified using featureCounts (-s 0) with GENCODE M27 annotation
Assembly: GRCm39 (mm39)
Supplementary files format and content: featureCounts.d3.mm39.vM27.txt
Supplementary files format and content: featureCounts.d5.mm39.vM27.WT.txt
Supplementary files format and content: featureCounts.d8.mm39.vM27.final.txt
|
| |
|
| Submission date |
Mar 17, 2023 |
| Last update date |
Jun 13, 2023 |
| Contact name |
Bryan McDonald |
| E-mail(s) |
bmcdonald@salk.edu
|
| Organization name |
Salk Institute for Biological Studies
|
| Street address |
10010 N Torrey Pines Rd
|
| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE227634 |
Effect of Arid1a deletion in antiviral effector CD8+ T cells. [RNA-seq] |
| GSE228381 |
Canonical BAF complex activity shapes the enhancer landscape that licenses CD8+ T cell effector and memory fates |
|
| Relations |
| BioSample |
SAMN33800047 |
| SRA |
SRX19713266 |
