ATRX guards against aberrant differentiation in mesenchymal progenitor cells [CUT&RUN]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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
- 36 samples: 36 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
- ATRX guards against aberrant differentiation in mesenchymal progenitor cellsNucleic acids research · 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 GSE252531_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 PRJNA1061124 and SRA study SRP481434. 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 36 sample titles: 36 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.
- GSM8002625 clone4_H3_3_R1 (Cut&Run)
- GSM8002626 clone4_H3_3_R2 (Cut&Run)
- GSM8002627 clone4_H3_3_R3 (Cut&Run)
- GSM8002628 clone4_IgG_R1 (Cut&Run)
- GSM8002629 clone4_IgG_R2 (Cut&Run)
- GSM8002630 clone4_IgG_R3 (Cut&Run)
- GSM8002631 clone4_k27ac_R1 (Cut&Run)
- GSM8002632 clone4_k27ac_R2 (Cut&Run)
- GSM8002633 clone4_k27ac_R3 (Cut&Run)
- GSM8002634 clone4_k9me3_R1 (Cut&Run)
- GSM8002635 clone4_k9me3_R2 (Cut&Run)
- GSM8002636 clone4_k9me3_R3 (Cut&Run)
- GSM8002637 clone6_H3_3_R1 (Cut&Run)
- GSM8002638 clone6_H3_3_R2 (Cut&Run)
- GSM8002639 clone6_H3_3_R3 (Cut&Run)
- GSM8002640 clone6_IgG_R1 (Cut&Run)
- GSM8002641 clone6_IgG_R2 (Cut&Run)
- GSM8002642 clone6_IgG_R3 (Cut&Run)
- GSM8002643 clone6_k27ac_R1 (Cut&Run)
- GSM8002644 clone6_k27ac_R2 (Cut&Run)
- GSM8002645 clone6_k27ac_R3 (Cut&Run)
- GSM8002646 clone6_k9me3_R1 (Cut&Run)
- GSM8002647 clone6_k9me3_R2 (Cut&Run)
- GSM8002648 clone6_k9me3_R3 (Cut&Run)
- GSM8002649 WT_H3_3_R1 (Cut&Run)
- GSM8002650 WT_H3_3_R2 (Cut&Run)
- GSM8002651 WT_H3_3_R3 (Cut&Run)
- GSM8002652 WT_IgG_R1 (Cut&Run)
- GSM8002653 WT_IgG_R2 (Cut&Run)
- GSM8002654 WT_IgG_R3 (Cut&Run)
- GSM8002655 WT_k27ac_R1 (Cut&Run)
- GSM8002656 WT_k27ac_R2 (Cut&Run)
- GSM8002657 WT_k27ac_R3 (Cut&Run)
- GSM8002658 WT_k9me3_R1 (Cut&Run)
- GSM8002659 WT_k9me3_R2 (Cut&Run)
- GSM8002660 WT_k9me3_R3 (Cut&Run)
- GSE303343 A unified network systems approach uncovers a core program underlying T follicular helper cell differentiation [CUT&RUN] 48 samples shares cut, run
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run
- GSE278910 Pooled CRISPR screens with joint single-nucleus chromatin accessibility and transcriptome profiling [CUT&RUN] 30 samples shares cut, run
- GSE301512 Chromatin topology dynamics of dexamethasone-treated trabecular meshwork identifies 78 causal genes for intraocular pressure and primary open angle glaucoma [CUT&Run] 30 samples shares cut, run
- GSE253893 PAX translocations remodel mitochondrial metabolism through altered leucine usage in rhabdomyosarcoma [Cut&Run] 28 samples shares cut, run
- GSE267470 Dual targeting of processive transcription for Myc-driven circuitry in medulloblastoma [CUT&RUN] 12 samples shares cut, run
- GSE316989 Targeting CDK12/CYCLIN K induces a gene activation program which is mediated by P-TEFb [Cut&RUN] 10 samples shares cut, run
- GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples shares cut, run
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.