Transcription factor reorganization at chromatin secures myeloid progenitor cell survival in PU.1 downregulated leukemia [ChIP-seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 20 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
- Acute myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 20 samples: 20 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
- Redistribution of PU.1 partner transcription factor RUNX1 binding secures cell survival during leukemogenesisThe EMBO journal · 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 GSE251672_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 PRJNA1055046 and SRA study SRP479179. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 10 samples read as cases, 10 as controls.
How we read this: Read from 20 sample titles: 20 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.
- GSM7985860 control, RUNX1, rep1, batch1
- GSM7985861 control, RUNX1, rep2, batch1
- GSM7985862 control, RUNX1, rep3, batch1
- GSM7985863 knockdown, RUNX1, rep1, batch1
- GSM7985864 knockdown, RUNX1, rep2, batch1
- GSM7985865 control, IgG, rep1, batch1
- GSM7985866 control, IgG, rep2, batch1
- GSM7985867 control, IgG, rep3, batch1
- GSM7985868 knockdown, IgG, rep1, batch1
- GSM7985869 knockdown, IgG, rep2, batch1
- GSM7985870 control, RUNX1, rep4, batch2
- GSM7985871 control, RUNX1, rep5, batch2
- GSM7985872 control, RUNX1, rep6, batch2
- GSM7985873 knockdown, RUNX1, rep3, batch2
- GSM7985874 knockdown, RUNX1, rep4, batch2
- GSM7985875 knockdown, RUNX1, rep5, batch2
- GSM7985876 knockdown, RUNX1, rep6, batch2
- GSM7985877 control, IgG, rep4, batch2
- GSM7985878 knockdown, IgG, rep3, batch2
- GSM7985879 knockdown, IgG, rep4, batch2
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- GSE270185 Repurposing CD19-directed immunotherapies for pediatric t(8;21) acute myeloid leukemia 249 samples same disease briefing · shares leukemia
- GSE137574 Kevetrin induces apoptosis in TP53 wild-type and mutant acute myeloid leukemia cells 24 samples same disease briefing · shares leukemia
- GSE303795 Halofuginone exerts broad-spectrum cytotoxic effects by regulating p-eIF2α-S100A8/A9-calcium signaling, inhibiting global protein synthesis, and reversing the resistance of idarubicin in acute myeloid leukemia 6 samples same disease briefing · shares leukemia
- GSE129437 Genome-wde mapping of BRD9 binding sites and gene expression changes upon BRD9 knockdown 6 samples same disease briefing
- GSE122515 Bonn Dataset 3 of meta-analysis on AML classification, RNAseq dataset 0 samples same disease briefing
- GSE296190 Hypoxic regulation of chromatin and gene transcription [ChIP-seq] 84 samples shares transcription, chromatin, chip-seq
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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.