RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [ChIP-seq]
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: 8 distinct titles, 2 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.
- Paper
- RB loss modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactionsNature communications · 2026
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 GSE315529_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 PRJNA1398214 and SRA study SRP659669. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 10 sample titles: 8 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.
- GSM9430123 hTERT-RPE1, MED15, RB WT, G1
- GSM9430124 hTERT-RPE1, MED15, RB KO, G1
- GSM9430125 hTERT-RPE1, SMC3, RB WT, M (Eg5i)
- GSM9430126 hTERT-RPE1, SMC3, RB KO clone 1.7, M (Eg5i)
- GSM9430127 hTERT-RPE1, STAG1, RB WT, G1, biol rep 1
- GSM9430128 hTERT-RPE1, STAG1, RB WT, G1, biol rep 2
- GSM9430129 hTERT-RPE1, STAG1, RB KO, G1, biol rep 1
- GSM9430130 hTERT-RPE1, STAG1, RB KO, G1, biol rep 2
- GSM9430131 hTERT-RPE1, STAG2, RB WT, G1
- GSM9430132 hTERT-RPE1, STAG2, RB KO, G1
- GSE266412 RB modulates chromatin organization by regulating cohesin-dependent loops and enhancer-promoter interactions [HiChIP] 4 samples shares cohesin-dependent, enhancer-promoter, organization, interactions, regulating, modulates, chromatin
- GSE208685 Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1- bound enhancers through interactions with the EP400 chromatin remodeler [ChIP-Seq] 12 samples shares interactions, chromatin, chip-seq
- GSE263641 CTCF depletion uncouples the role of enhancer-promoter interactions and higher-order chromatin hubs in gene regulation during cellular differentiation. 137 samples shares enhancer-promoter, interactions, chromatin
- GSE271752 Macromolecular interactions dictate Polycomb-mediated epigenetic repression [ChIP-seq] 194 samples shares interactions, chip-seq
- GSE278977 Transcriptional programs of cell identity and p53-induced stress responses are associated with distinctive features of spatial genome organization [ChIP-seq] 80 samples shares organization, chip-seq
- GSE249439 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response [ATAC-seq] 48 samples shares organization, chromatin
- GSE275238 LINE1 and PRC2 control nucleolar organization and repression of the 8C-state in human ESCs [ChIP-seq_primed,RSeT,RSeT+DT_hESCs] 18 samples shares organization, chip-seq
- GSE249492 ARID1A regulates DSB repair through chromatin organization and its deficiency triggers DNA damage-mediated immune response 280 samples shares organization, chromatin
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.