Chromatin accessibility of hematopoietic stem/progenitor cells (HSPCs) derived from MDS patients before and after disease progression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 2 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
- Homo sapiens (human)
- Topic
- Myelodysplastic syndromesThis series is part of our curated briefing on it.
- Samples
- 2 samples
- 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
- A heterozygous CEBPA mutation disrupting the bZIP domain in a RUNX1 and SRSF2 mutational background causes MDS disease progressionNature communications · 2025
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 GSE298729_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 PRJNA1271021 and SRA study SRP589275. Searching any of these in the dataset finder brings you back here.
The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.
+ 2 more — browse all 2 samples with per-sample file links →
- GSE284647 The genotype-integrated gene expression profile at the single-cell level of bone marrow CD34-positive hematopoietic stem and progenitor cells (HSPCs) from a patient with myelodysplastic neoplasms (MDS) harboring germline and somatic DDX41 variants. 1 samples same disease briefing · shares mds, hematopoietic, progenitor, hspcs
- GSE298020 PU.1-Activated Genomic Regions Define Low-risk MDS Subsets Characterized by Immune Dysregulation and Disease Progression. 493 samples same disease briefing · shares mds, progression
- GSE275000 Clinical response to azacitidine in MDS is associated with distinct DNA methylation changes in HSPCs 104 samples same disease briefing · shares mds, hspcs
- GSE291718 Analysis of chromatin accessibility relative to epigenetic features of azacitidine response in high-risk myelodysplastic syndrome 56 samples same disease briefing · shares accessibility, chromatin
- GSE248804 MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ChIP-Seq human] 12 samples same disease briefing · shares accessibility, chromatin
- GSE248802 MED16 negatively regulates erythropoiesis and myelopoiesis through modulation of chromatin accessibility [ATAC-Seq human] 8 samples same disease briefing · shares accessibility, chromatin
- GSE265824 Human iPSCs-based modeling unveils a dominant role of SETBP1 mutation in shaping stable chromatin accessibility landscape in GATA2 deficiency 25 samples same disease briefing · shares accessibility, chromatin
- GSE270760 PRC2-mediated apoptosis evasion is a therapeutic target of MDS/AML harboring inv(3)/t(3;3) and monosomy 7 (CUT&Tag) 24 samples same disease briefing · shares mds
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.