|
| Status |
Public on Feb 21, 2024 |
| Title |
TCF1+CD8+ T cells, aCD3/CD28 beads, IL-2, PGE2, rep3 |
| 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: aCD3/CD28 Beads + IL-2, PGE2
replicate: 3
|
| 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 |
IL2LoBP3
|
| 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 |
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 |
|
| Relations |
| BioSample |
SAMN34436223 |
| SRA |
SRX20143769 |
