Heterochromatin Protein ERH represses alternative cell fates during early mammalian differentiation [CUT&RUN]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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
- 10 samples: 3 × BJ fibroblast siControl H3K9me3 CUT&RUN vs 3 × BJ fibroblast siERH H3K9me3 CUT&RUN vs 2 × BJ fibroblast siControl+OSKM SOX2 CUT&RUN vs 2 × BJ fibroblast siERH+OSKM SOX2 CUT&RUNGroups 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 GSE268961_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 PRJNA1119505 and SRA study SRP511439. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 10 sample titles; they account for 10 of them. 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.
- GSM8303589 BJ fibroblast siControl H3K9me3 CUT&RUN rep1 BJ fibroblast siControl…
- GSM8303590 BJ fibroblast siControl H3K9me3 CUT&RUN rep2 BJ fibroblast siControl…
- GSM8303591 BJ fibroblast siControl H3K9me3 CUT&RUN rep3 BJ fibroblast siControl…
- GSM8303592 BJ fibroblast siERH H3K9me3 CUT&RUN rep1 BJ fibroblast siERH H3K…
- GSM8303593 BJ fibroblast siERH H3K9me3 CUT&RUN rep2 BJ fibroblast siERH H3K…
- GSM8303594 BJ fibroblast siERH H3K9me3 CUT&RUN rep3 BJ fibroblast siERH H3K…
- GSM8303595 BJ fibroblast siControl+OSKM SOX2 CUT&RUN rep1 BJ fibroblast siControl…
- GSM8303596 BJ fibroblast siControl+OSKM SOX2 CUT&RUN rep2 BJ fibroblast siControl…
- GSM8303597 BJ fibroblast siERH+OSKM SOX2 CUT&RUN rep1 BJ fibroblast siERH+OSK…
- GSM8303598 BJ fibroblast siERH+OSKM SOX2 CUT&RUN rep2 BJ fibroblast siERH+OSK…
- 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
- GSE269555 Targeting the oncohistone-ASCL1 axis disrupts plasticity and suppresses pediatric gliomas [CUT&RUN] 39 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
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.