Mechanosensing by T cells promotes a tissue-resident memory transcriptional program
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 × WT_CD8_d0_naive vs 3 × WT_CD8_d4_media vs 3 × WT_CD8_d4_Nutragen2mgmL vs 3 × WT_CD8_d4_RatCol2mgmLGroups 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.
Read the full summary ↓
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 GSE278556_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 PRJNA1167774 and SRA study SRP536082. 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.
- GSM8548805 WT_CD8_d0_naive_001 WT_CD8_d0_naive
- GSM8548806 WT_CD8_d0_naive_002 WT_CD8_d0_naive
- GSM8548807 WT_CD8_d0_naive_003 WT_CD8_d0_naive
- GSM8548808 WT_CD8_d4_media_001 WT_CD8_d4_media
- GSM8548809 WT_CD8_d4_media_002 WT_CD8_d4_media
- GSM8548810 WT_CD8_d4_media_003 WT_CD8_d4_media
- GSM8548811 WT_CD8_d4_Nutragen2mgmL_001 WT_CD8_d4_Nutragen2mgmL
- GSM8548812 WT_CD8_d4_Nutragen2mgmL_002 WT_CD8_d4_Nutragen2mgmL
- GSM8548813 WT_CD8_d4_Nutragen2mgmL_003 WT_CD8_d4_Nutragen2mgmL
- GSM8548814 WT_CD8_d4_RatCol2mgmL_001 WT_CD8_d4_RatCol2mgmL
- GSM8548815 WT_CD8_d4_RatCol2mgmL_002 WT_CD8_d4_RatCol2mgmL
- GSM8548816 WT_CD8_d4_RatCol2mgmL_003 WT_CD8_d4_RatCol2mgmL
- GSE279117 HIF1α deletion promotes mitochondrial repurposing in bone marrow-derived macrophages, but not in tissue-resident alveolar macrophages 24 samples shares tissue-resident, promotes
- GSE334940 Tissue nanotransfection-mediated induction of neurogenic programs promotes myoprotective responses in denervated skeletal muscle 15 samples shares promotes, program
- GSE341988 Sequential pathogen exposure normalizes the brain neuroimmune microenvironment and reveals a tissue-resident memory CD8 T cell-microglia axis shaping adult neurogenesis 8 samples shares tissue-resident, memory
- GSE342096 Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence 37 samples shares program, memory
- GSE278100 Foxa1-Mediated Chromatin Remodeling and Enhancer Reprogramming Promotes Gemcitabine Resistance in Pancreatic Cancer 54 samples shares promotes, program
- GSE316619 Epigenetic memory of colitis promotes tumour growth 47 samples shares promotes, memory
- GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares promotes, memory
- GSE279042 Reprogramming of epidermal keratinocytes by PITX1 transforms the cutaneous cellular landscape and promotes wound healing [CUT&Tag] 30 samples shares promotes, program
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.