|
| Status |
Public on Aug 14, 2023 |
| Title |
CD4 T cells from spleen transduced with empty vector replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
spleen
|
| Organism |
Mus musculus |
| Characteristics |
tissue: spleen
cell type: CD4 T cells
genotype: WT
treatment: anti-CD3, soluble anti-CD28 and recombinant human anti-CD28
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Resulting cells were washed twice with 1x sterile PBS the pellets were resuspended in 500uL of Trizol reagent (Applied Biosystems) and RNA-isolation was carried out as per manufacturer’s instructions.
RNA from these cells was sent to Novogene for library preparation and sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw sequencing quality was checked using fastqc. Adapters were trimmed later.
Alignment and RNA expression level calculation was carried out using bowtie2 and RSEM (--bowtie-n 1 --bowtie-m 100). Reference transcript used in alignment was mm10.
DESeq2 was used to identify the differential expressed genes between CD4+ T cells transduced with TOX retrovirus and with Empty Vector retrovirus with default parameters.
Differentially expressed genes (DEGs) were sorted based on significant level (log2(fold change)*-log2(p-value)).
Assembly: mm10
Supplementary files format and content: tab-delmited file including TPM from all samples and separte RSEM result for each sample.
|
| |
|
| Submission date |
Aug 08, 2023 |
| Last update date |
Aug 14, 2023 |
| Contact name |
D. Alejandro Canaria |
| E-mail(s) |
dcanaria@purdue.edu
|
| Organization name |
Purdue University
|
| Street address |
201 S University St
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE240348 |
TOX induces T cell IL-10 production in a BATF-dependent manner |
|
| Relations |
| BioSample |
SAMN36890285 |
| SRA |
SRX21298455 |
