Chronic TCR signaling-driven suppression of FOXO1-KLHL6 axis promotes T cell exhaustion
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × Naive vs 3 × 24h vs 3 × 48h vs 3 × 72hGroups 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 GSE317019_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 PRJNA1405681 and SRA study SRP664814. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9463896 Naive1 Naive
- GSM9463897 Naive2 Naive
- GSM9463898 Naive3 Naive
- GSM9463899 24h-1 24h
- GSM9463900 24h-2 24h
- GSM9463901 24h-3 24h
- GSM9463902 48h-1 48h
- GSM9463903 48h-2 48h
- GSM9463904 48h-3 48h
- GSM9463905 72h-1 72h
- GSM9463906 72h-2 72h
- GSM9463907 72h-3 72h
- GSE277648 Stem cell-like CD8+ T cells lacking PD-1 adapt to chronic stimulation by reducing TCR signaling and self-renewal capacity [RNA-seq] 16 samples shares tcr, chronic
- GSE309052 The TCR-SUB1-DOCK2 Signaling Axis Governs Autoimmunity by Regulating CD4+ T Cell Migratory Capacity 14 samples shares tcr, axis
- GSE250590 Suppression of the mRNA export pathway dampens viral mimicry response and promotes tumor immune evasion [RNA-seq] 92 samples shares suppression, promotes
- GSE249867 KRAS-mediated upregulation of CIP2A promotes suppression of PP2A-B56a to initiate pancreatic cancer development [RNA-Seq] 16 samples shares suppression, promotes
- GSE328178 Genetic suppression of myeloid receptor Clec7a attenuates microglia neuroinflammation and promotes microglial phagocytosis to delay disease progression in ALS models 14 samples shares suppression, promotes
- GSE319419 Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer [RNA-Seq Hi-Myc mice] 12 samples shares suppression, axis
- GSE263901 The Rapid Evolution of Chronic Inflammation to Tolerance / Immune Suppression: Mapping Bidirectional Checkpoints 11 samples shares suppression, chronic
- GSE180075 Type I interferon limits ILC2 effector functions through suppression of the CCR8-CCL1/CCL8 axis 10 samples shares suppression, axis
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.