Analysis of different mouse P14 CD8+T cell subset gene signatures in presence and absence of Tim-3+ Treg during LCMV CL13 infection
RNA-seq (gene expression) · mouse · 18 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
- 18 samples: 6 conditions, mostly in triplicateGroups 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.
- Paper
- Tim-3 Is Required for Regulatory T Cell-Mediated Promotion of T Cell Exhaustion and Viral Persistence during Chronic Lymphocytic Choriomeningitis Virus InfectionJournal of immunology (Baltimore, Md. : 1950) · 2024
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 GSE254211_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 PRJNA1069017 and SRA study SRP485942. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 6 replicated groups read from 18 sample titles; they account for 17 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.
- GSM8036068 PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 1 PD-1-Tim-3- P14 T cells…
- GSM8036069 PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 1 PD-1+Tim-3- P14 T cells…
- GSM8036070 PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 1 PD-1+Tim-3+ P14 T cells…
- GSM8036071 PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 2 PD-1-Tim-3- P14 T cells…
- GSM8036072 PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 2 PD-1+Tim-3- P14 T cells…
- GSM8036073 PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 2 PD-1+Tim-3+ P14 T cells…
- GSM8036074 PD-1-Tim-3- P14 T cells isolated from Cre-only mouse, replicate 3 PD-1-Tim-3- P14 T cells…
- GSM8036075 PD-1+Tim-3- P14 T cells isolated from Cre-only mouse, replicate 3 PD-1+Tim-3- P14 T cells…
- GSM8036076 PD-1+Tim-3+ P14 T cells isolated from Cre-only mouse, replicate 3 PD-1+Tim-3+ P14 T cells…
- GSM8036077 PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1 PD-1-Tim-3- P14 T cells…
- GSM8036078 PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1 PD-1+Tim-3- P14 T cells…
- GSM8036079 PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 1 PD-1+Tim-3+ P14 T cells…
- GSM8036080 PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 2 PD-1-Tim-3- P14 T cells…
- GSM8036081 PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 2 PD-1+Tim-3- P14 T cells…
- GSM8036082 PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse replicate 2
- GSM8036083 PD-1-Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3 PD-1-Tim-3- P14 T cells…
- GSM8036084 PD-1+Tim-3- P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3 PD-1+Tim-3- P14 T cells…
- GSM8036085 PD-1+Tim-3+ P14 T cells isolated from Treg-specific Tim-3 KO mouse, replicate 3 PD-1+Tim-3+ P14 T cells…
- GSE300892 Cell-intrinsic Tim-3 is Required for Optimal CD8 Response to Acute LCMV Infection [RNAseq] 10 samples shares tim-3, lcmv, cd8
- GSE301002 Cell-intrinsic Tim-3 is Required for Optimal CD8 Response to Acute LCMV Infection 9 samples shares tim-3, lcmv, cd8
- GSE226067 scATAC-seq of antigen-specific CD8+ T cells from different time-course of LCMV-Armstrong infected mice 5 samples shares lcmv, cd8, different
- GSE297040 ZFP148 is a transcriptional regulator of effector CD8+ T cell differentiation [single-cell_multiome] 4 samples shares p14, cd8, different
- GSE296837 IFN-γ-induced PD-L1+ and MHC II+ macrophages and Tim-3+ tumor-reactive CD8+ T cells predict a positive response to anti-PD-1 therapy in tumor-bearing mice 28 samples shares tim-3, cd8
- GSE297330 TNFR2 loss prevents TOX upregulation in CD8+TIM3+ T cells and affords improved responses to tumor and chronic LCMV 19 samples shares lcmv, cd8
- GSE284025 Bulk RNA-sequencing of CD7+ and CD7- CD8 T cells from chronic LCMV infection 18 samples shares lcmv, cd8
- GSE268071 Bulk RNA-seq analysis of exhausted CD8 T cell subsets during LCMV clone 13 infection 16 samples shares lcmv, cd8
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.