Epigenetic Profiling of T-bet/Runx3 Double Knockout Models via ATAC-seq and Cut&Run in Antiviral CD8+T Cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 9 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 9 samples: 3 × ATAC-seq of Runx3 KO vs 3 × ATAC-seq of Tbet and Runx3 KO vs 3 × Chip-seq of Tbet with Runx3 KOGroups 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 GSE308991_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1333556 and SRA study SRP625742. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM9105449 ATAC-seq of Runx3 KO 1 ATAC-seq of Runx3 KO
- GSM9105450 ATAC-seq of Runx3 KO 2 ATAC-seq of Runx3 KO
- GSM9105451 ATAC-seq of Runx3 KO 3 ATAC-seq of Runx3 KO
- GSM9105452 ATAC-seq of Tbet and Runx3 KO 1 ATAC-seq of Tbet and Ru…
- GSM9105453 ATAC-seq of Tbet and Runx3 KO 2 ATAC-seq of Tbet and Ru…
- GSM9105454 ATAC-seq of Tbet and Runx3 KO 3 ATAC-seq of Tbet and Ru…
- GSM9105461 Chip-seq of Tbet with Runx3 KO 1 Chip-seq of Tbet with R…
- GSM9105462 Chip-seq of Tbet with Runx3 KO 2 Chip-seq of Tbet with R…
- GSM9105463 Chip-seq of Tbet with Runx3 KO 3 Chip-seq of Tbet with R…
- GSE342312 T-bet and Runx3 orchestrate effector CD8 T cell differentiation and lineage fidelity through cooperative and distinct chromatin regulatory mechanisms [Multi-omics] 40 samples shares runx3, cd8, t-bet
- GSE274865 Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [CUT&Tag] 36 samples shares cd8, epigenetic
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares cd8, atac-seq
- GSE157232 The CD8+ T cell tolerance checkpoint triggers a transcriptionally and epigenetically distinct differentiation state defined by protein translation defects 30 samples shares cd8, epigenetic
- GSE298001 Stage-specific Epigenetic Priming Amplifies Gene Activation During Lineage Commitment [ATAC-Seq] 36 samples shares epigenetic, atac-seq
- GSE236575 Adipose tissue retains an epigenetic memory of obesity after weight loss [ATAC-seq] 22 samples shares epigenetic, atac-seq
- GSE271883 Maternal high-fat diet alters Tet-mediated epigenetic regulation during heart development [ATAC-Seq] 12 samples shares epigenetic, atac-seq
- GSE252551 Disease-associated astrocyte epigenetic memory promotes CNS pathology [ATAC-Seq and RNA-Seq] 32 samples shares epigenetic, atac-seq
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.