Bulk RNA-seq analysis of exhausted CD8 T cell subsets during LCMV clone 13 infection
RNA-seq (gene expression) · mouse · 16 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 4 × TIM3+ CX3CR1+ cells, KO vs 4 × TIM3+ CX3CR1– cells, KO vs 4 × TIM3+ CX3CR1+ cells, WT vs 4 × TIM3+ CX3CR1– cells, WTGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE268071_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1108758 and SRA study SRP506183. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 16 samples.
How we read this: 4 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8285455 TIM3+ CX3CR1+ cells, KO 874 TIM3+ CX3CR1+ cells, KO
- GSM8285456 TIM3+ CX3CR1– cells, KO 874 TIM3+ CX3CR1– cells, KO
- GSM8285457 TIM3+ CX3CR1+ cells, KO 876 TIM3+ CX3CR1+ cells, KO
- GSM8285458 TIM3+ CX3CR1– cells, KO 876 TIM3+ CX3CR1– cells, KO
- GSM8285459 TIM3+ CX3CR1+ cells, KO 940 TIM3+ CX3CR1+ cells, KO
- GSM8285460 TIM3+ CX3CR1– cells, KO 940 TIM3+ CX3CR1– cells, KO
- GSM8285461 TIM3+ CX3CR1+ cells, KO 945 TIM3+ CX3CR1+ cells, KO
- GSM8285462 TIM3+ CX3CR1– cells, KO 945 TIM3+ CX3CR1– cells, KO
- GSM8285463 TIM3+ CX3CR1+ cells, WT 849 TIM3+ CX3CR1+ cells, WT
- GSM8285464 TIM3+ CX3CR1– cells, WT 849 TIM3+ CX3CR1– cells, WT
- GSM8285465 TIM3+ CX3CR1+ cells, WT 850 TIM3+ CX3CR1+ cells, WT
- GSM8285466 TIM3+ CX3CR1– cells, WT 850 TIM3+ CX3CR1– cells, WT
- GSM8285467 TIM3+ CX3CR1+ cells, WT 853 TIM3+ CX3CR1+ cells, WT
- GSM8285468 TIM3+ CX3CR1– cells, WT 853 TIM3+ CX3CR1– cells, WT
- GSM8285469 TIM3+ CX3CR1+ cells, WT 856 TIM3+ CX3CR1+ cells, WT
- GSM8285470 TIM3+ CX3CR1– cells, WT 856 TIM3+ CX3CR1– cells, WT
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares cd8, exhausted, subsets
- GSE215759 Mettl3-dependent m6A modification is essential for effector differentiation and memory formation of CD8+ T cells [RNA-seq] 15 samples shares cd8, rna-seq
- GSE275974 SATB1 is a key regulator of quiescence in stem-like CD8+ T cells [RNA-seq] 10 samples shares cd8, rna-seq
- GSE235005 Nutrient-driven histone code determines exhausted CD8+ T cell fates [ChIP-seq] 50 samples shares cd8, exhausted
- GSE285187 A core stemness program in exhausted CD8+ T cells 24 samples shares cd8, exhausted
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq, bulk
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq, bulk
- GSE228960 Bulk RNA-Seq from kidneys of uninephrectomized db/db mice as a model of severe diabetic kidney disease 28 samples shares rna-seq, bulk
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.