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Sample GSM7256669 Query DataSets for GSM7256669
Status Public on Feb 21, 2024
Title TCF1+CD8+ T cells, no beads, IL-2, PGE2, rep1
Sample type SRA
 
Source name spleen
Organism Mus musculus
Characteristics tissue: spleen
developmental stage: Naive CD8 T cells isolated from mouse spleen and then differentiated into TCF1+CD8+T cells
cell type: Murine in vitro differentiated TCF1+CD8+ T cells
genotype: C57BL/6J
treatment: IL-2, PGE2
replicate: 1
Treatment protocol In vitro differentiated and repetitively stimulated antigen-experienced TCF1+CD8+ T cells were pre-incubated with or without PGE2 (100 ng/mL) for 1 hour at 37°C. Subsequently, the cells were stimulated for an additional 4 hours with low dose IL-2 (85 U/ml) or the combination of low dose IL-2 and aCD3/CD28 beads (1 bead/cell).
Growth protocol Naive mouse CD8+ T cells were isolated from mouse spleens and then differentiated into TCF1+CD8+ T cells over 4 days.
Extracted molecule total RNA
Extraction protocol RNA was isolated using Total RNA Miniprep (Monarch)
Isolated RNA was sent to Novogene for library preparation. Libraries were prepared using mRNA Library preparation Poly A enrichment and The NEB Next® Ultra™ RNA Library Prep Kit (i7 index read, 8bp; i5 index read, 8bp).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description IL2LoP1
Data processing Quality control: Reads containing adapter, poly-N, and low quality reads were removed from raw reads using an in-inhouse perl script by Novogene. Q20, Q30, and GC contet of the clean data were calculated. All further data analyses were based on the clean data set.
Clean reads (paired-end) were aligned to the reference genome (Mus Musculus(GRCm38/mm10)) using Hisat2 v2.0.5.
For the quantification of gene espression levels, featureCounts v1.5.0-p3 was used. FPKM of each gene was calculated based on the length and reads count.
Differential expression analysis was performed using DESeq2 R package (1.20.0). The obtained p-values were adjusted using the Benjamini and Hochberg´s apporach for controlling the FDR. Genes were assigned as differentitally expressed when adjusted p-value reached <=0.05 (found by DESeq2).
Assembly: GRCm38/mm10
Supplementary files format and content: The feature_counts.xls files is a Microsoft Excel Binary File containing gene counts as rows and samples and gene features as columns. The gene_fpkm.xls is a Microsoft Excel Binary File containing gene FPKM as rows and samples and gene features as columns.
 
Submission date Apr 29, 2023
Last update date Feb 21, 2024
Contact name Gustavo P. de Almeida
E-mail(s) gustavo.almeida@tum.de
Organization name Technical University of Munich
Department Division of Animal Physiology and Immunology
Street address Weihenstephaner Berg 3
City Freising
State/province Bavaria
ZIP/Postal code 85354
Country Germany
 
Platform ID GPL24247
Series (2)
GSE231301 RNA sequencing of murine in vitro differentiated and repetitively activated, antigen-experienced TCF1+CD8+ T cells after PGE2 treatment and stimulation [bulk RNA-Seq]
GSE231340 PGE2 curtails IL-2-dependent effector expansion from tumour-infiltrating stem-like CD8+ T cells to promote cancer immune escape
Relations
BioSample SAMN34436233
SRA SRX20143759

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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