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Sample GSM7696614 Query DataSets for GSM7696614
Status Public on Aug 14, 2023
Title CD4 T cells from spleen transduced with retroviruses encoding TOX 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, transduced with retrovirus encoding TOX
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
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
BioSample SAMN36890283
SRA SRX21298457

Supplementary file Size Download File type/resource
GSM7696614_PS4939-147.R12.genes.results.gz 466.5 Kb (ftp)(http) RESULTS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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