cPRC1.2 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene Activation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 43 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
- 43 samples: 13 conditions, mostly in duplicateGroups 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
- PRC1 and CTCF-Mediated Transition from Poised to Active Chromatin Loops Drives Bivalent Gene ActivationbioRxiv : the preprint server for biology · 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 GSE278946_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 PRJNA1169811 and SRA study SRP537246. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 26 samples.
How we read this: 13 replicated groups read from 43 sample titles; they account for 26 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.
- GSM8558255 RNA-seq ESC WT 1 RNA-seq ESC WT
- GSM8558256 RNA-seq ESC WT 2 RNA-seq ESC WT
- GSM8558257 RNA-seq ESC Pcgf2 KO 1 RNA-seq ESC Pcgf2 KO
- GSM8558258 RNA-seq ESC Pcgf2 KO 2 RNA-seq ESC Pcgf2 KO
- GSM8558259 RNA-seq ESC Phc1 KO 1 RNA-seq ESC Phc1 KO
- GSM8558260 RNA-seq ESC Phc1 KO 2 RNA-seq ESC Phc1 KO
- GSM8558261 RNA-seq ESC Phc1-SAM KO 1 RNA-seq ESC Phc1-SAM KO
- GSM8558262 RNA-seq ESC Phc1-SAM KO 2 RNA-seq ESC Phc1-SAM KO
- GSM8558263 RNA-seq EB day 3 WT 1 RNA-seq EB day 3 WT
- GSM8558264 RNA-seq EB day 3 WT 2 RNA-seq EB day 3 WT
- GSM8558265 RNA-seq EB day 3 Pcgf2 KO 1 RNA-seq EB day 3 Pcgf2 …
- GSM8558266 RNA-seq EB day 3 Pcgf2 KO 2 RNA-seq EB day 3 Pcgf2 …
- GSM8558267 RNA-seq EB day 8 WT 1 RNA-seq EB day 8 WT
- GSM8558268 RNA-seq EB day 8 WT 2 RNA-seq EB day 8 WT
- GSM8558269 RNA-seq EB day 8 Pcgf2 KO 1 RNA-seq EB day 8 Pcgf2 …
- GSM8558270 RNA-seq EB day 8 Pcgf2 KO 2 RNA-seq EB day 8 Pcgf2 …
- GSM8558271 RNA-seq NPC WT 1 RNA-seq NPC WT
- GSM8558272 RNA-seq NPC WT 2 RNA-seq NPC WT
- GSM8558273 RNA-seq NPC Pcgf2 KO 1 RNA-seq NPC Pcgf2 KO
- GSM8558274 RNA-seq NPC Pcgf2 KO 2 RNA-seq NPC Pcgf2 KO
- GSM8558275 RNA-seq NPC Phc1 KO 1 RNA-seq NPC Phc1 KO
- GSM8558276 RNA-seq NPC Phc1 KO 2 RNA-seq NPC Phc1 KO
- GSM8558277 RNA-seq NPC Phc1-SAM KO 1 RNA-seq NPC Phc1-SAM KO
- GSM8558278 RNA-seq NPC Phc1-SAM KO 2 RNA-seq NPC Phc1-SAM KO
- GSM8558279 ChIP-seq ESC WT Input ChIP-seq ESC WT Input
- GSM8558280 ChIP-seq ESC WT H2AK119ub1
- GSM8558281 ChIP-seq ESC WT Ring1b
- GSM8558282 ChIP-seq ESC Pcgf2-KO Input 1
- GSM8558283 ChIP-seq ESC Pcgf2-KO H2AK119ub1
- GSM8558284 ChIP-seq ESC Pcgf2-KO Ring1b
- GSM8558285 Hi-C ESC WT
- GSM8558286 Hi-C ESC Pcgf2 KO
- GSM8611920 Hi-C NPC Pcgf2 KO
- GSM9186575 ChIP-seq ESC WT Input 2 ChIP-seq ESC WT Input
- GSM9186576 ChIP-seq ESC WT Ctcf
- GSM9186577 ChIP-seq ESC Pcgf2 KO Input 2
- GSM9186578 ChIP-seq ESC Pcgf2 KO Ctcf
- GSM9186579 ChIP-seq ESC Irx3-anchor KO Input
- GSM9186580 ChIP-seq ESC Irx3-anchor KO Ctcf
- GSM9186587 ChIP-seq U2OS siControl Input
+ 3 more — browse all 43 samples with per-sample file links →
- GSE299957 MeCP2 gene dosage-dependent neurodevelopmentally restricted defects arise by SWI/SNF-mediated aberrant activation of cell fate-determining bivalent genes 50 samples shares activation, bivalent
- GSE80006 Single-cell Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition 246 samples shares transition, chromatin
- GSE101571 Analysis of chromatin landscapes in early human development reveals epigenetic transition during ZGA 55 samples shares transition, chromatin
- GSE240603 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs 144 samples shares activation
- GSE240599 An eRNA Transcription Checkpoint For Diverse Signal-dependent Enhancer Activation Programs 130 samples shares activation
- GSE244947 NOTCH1 reverses immune suppression in small cell lung cancer through reactivation of STING 87 samples shares activation
- GSE296242 Sustained MYB activity drives emergent enhancer activation and precise enhancer-promoter interactions 81 samples shares activation
- GSE292300 A core transcriptional regulatory circuitry controls super-enhancer-driven activation of LGR5 in colorectal cancer: ChIP-seq 76 samples shares activation
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.