Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [ATAC-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 16 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
- 16 samples: 16 samples, each with a distinct title — no replicated groupsGroups 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
- Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapyScience (New York, N.Y.) · 2024
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 GSE274863_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 PRJNA1148210 and SRA study SRP526442. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 16 sample titles: 16 distinct titles with little repetition. 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.
- GSM8459569 Rosa, replicate 1, ATAC
- GSM8459570 Rosa, replicate 2, ATAC
- GSM8459571 Asxl1, replicate 1, ATAC
- GSM8459572 Asxl1, replicate 2, ATAC
- GSM8459573 Rosa Ly108, replicate 1, ATAC
- GSM8459574 Rosa Ly108, replicate 2, ATAC
- GSM8459575 Rosa Tim3, replicate 1, ATAC
- GSM8459576 Rosa Tim3, replicate 2, ATAC
- GSM8459577 Asxl1 Ly108, replicate 1, ATAC
- GSM8459578 Asxl1 Ly108, replicate 2, ATAC
- GSM8459579 Asxl1 Ly108, replicate 3, ATAC
- GSM8459580 Asxl1 Ly108, replicate 4, ATAC
- GSM8459581 Asxl1 Tim3, replicate 1, ATAC
- GSM8459582 Asxl1 Tim3, replicate 2, ATAC
- GSM8459583 Asxl1 Tim3, replicate 3, ATAC
- GSM8459584 Asxl1 Tim3, replicate 4, ATAC
- GSE274865 Epigenetic regulators of clonal hematopoiesis control CD8 T cell stemness during immunotherapy [CUT&Tag] 36 samples shares cd8, hematopoiesis, immunotherapy, epigenetic, regulators, stemness, control
- GSE337898 ATAC-seq profiling of lineage-traced exhausted and memory-like CD8+ T cell subsets during tumor progression 24 samples shares cd8, atac-seq
- GSE304763 A pan-immunotherapy signature to predict intratumoral CD8+ T cell expansions [scTCR_immunotherapies] 91 samples shares cd8, immunotherapy
- GSE255887 HDAC1 controls the generation and maintenance of effector-like CD8+ T cells during chronic viral infection 76 samples shares cd8, control
- GSE302682 Sleeping Beauty mutagenesis identifies BACH2 and other regulators promoting CD8+ T cell persistence and effector function under tumor-associated chronic antigen stimulation - RNAseq 66 samples shares cd8, regulators
- GSE334890 Discovery of Tcf7 regulators with clonally-resolved CRISPR screens identifies Trim28 as a mediator of CD8 T cell differentiation in tumors 48 samples shares cd8, regulators
- GSE261250 Gfi1 controls the formation of effector CD8+ T cells during chronic infection and cancer 47 samples shares cd8, control
- GSE342096 Distinct activation programs in naïve and memory CD8 T cells govern progeny stemness and effector persistence 37 samples shares cd8, stemness
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.