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Status |
Public on Feb 21, 2024 |
Title |
TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep2 |
Sample type |
SRA |
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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: aCD3/CD28 Beads + IL-2, PGE2 replicate: 2
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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).
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Growth protocol |
Naive mouse CD8+ T cells were isolated from mouse spleens and then differentiated into TCF1+CD8+ T cells over 4 days.
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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).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
Description |
IL2LoBP2
|
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.
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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 |
Liesel-Beckmann-Str. 1
|
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 |
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Relations |
BioSample |
SAMN34436224 |
SRA |
SRX20143768 |