Mutant p53 alters chromatin accessibility in hematopoietic stem and progenitor cells.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 37 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)
- Samples
- 37 samples: 26 distinct titles, 6 of them repeatedGroups 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 GSE261634_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 PRJNA1088138 and SRA study SRP495308. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 5 samples read as cases, 10 as controls.
How we read this: Read from 37 sample titles: 26 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.
- GSM8147655 WT#1-LSKs
- GSM8147656 WT#2-LSKs
- GSM8147657 R248W#1-LSKs
- GSM8147658 R248W#2-LSKs
- GSM8147659 WT#1-PBS
- GSM8147660 WT#2-PBS
- GSM8147661 WT#3-PBS
- GSM8147662 WT#4-PBS
- GSM8147663 R248W#-1-PBS
- GSM8147664 R248W#-2-PBS
- GSM8147665 R248W#-3-PBS
- GSM8147666 R248W#-4-PBS
- GSM8147667 WT#1-IL1Beta
- GSM8147668 WT#2-IL1Beta
- GSM8147669 WT#3-IL1Beta
- GSM8147670 WT#4-IL1Beta
- GSM8147671 R248W#1-IL1Beta
- GSM8147672 R248W#2-IL1Beta
- GSM8147673 R248W#3-IL1Beta
- GSM8147674 R248W#4-IL1Beta
- GSM8147675 Aged-WT#1
- GSM8147676 Aged-WT#2
- GSM8147677 Aged-R248W#1
- GSM8147678 Aged-R248W#2
- GSM8153979 CD34_MIGR1_1
- GSM8153980 CD34_MIGR1_2
- GSM8153981 CD34_MIGR1_3
- GSM8153982 CD34_MIGR1_4
- GSM8153983 CD34_R248W_1
- GSM8153984 CD34_R248W_2
- GSM8153985 CD34_R248W_3
- GSM8153986 CD34_R248W_4
- GSM8153987 Primary human BM cells, no-TP53 mutations, patient 1
- GSM8153988 Primary human BM cells, no-TP53 mutations, patient 2
- GSM8153989 Primary human BM cells, TP53 mutation, patient 1
- GSM8153990 Primary human BM cells, TP53 mutation, patient 2
- GSM8153991 Primary human BM cells, TP53 mutation, patient 5
- GSE296783 Transcriptional changes and epigenetic landscapes in fetal hematopoietic stem and progenitor cells with DDX21 knockout 12 samples shares hematopoietic, progenitor, stem
- GSE216612 Gene expression profiles of hematopoietic stem/progenitor cells after stimulating CCL2. 2 samples shares hematopoietic, progenitor, stem
- GSE248639 Nynrin preserves hematopoietic stem cell function by inhibiting the mitochondrial permeability transition pore opening. 19 samples shares hematopoietic, stem
- GSE65360 Single-cell chromatin accessibility data using scATAC-seq 1632 samples shares accessibility, chromatin
- GSE320163 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [ATAC-Seq] 377 samples shares chromatin, stem
- GSE320162 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [RNA-Seq] 347 samples shares chromatin, stem
- GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis 166 samples shares progenitor, mutant
- GSE295715 Leukemia-mutated proteins PHF6 and PHIP form a chromatin complex that represses acute myeloid leukemia stemness 90 samples shares chromatin, stem
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.