Profiling of PRC1 and PRC2 occupancy reveals the preponderant role of PRC1 in regulating the limb development program
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 24 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
- Mus musculus (mouse)
- Samples
- 24 samples: 24 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.
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 GSE186579_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 PRJNA774641 and SRA study SRP343172. 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 24 sample titles: 24 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.
- GSM5655988 e12.5_mouse_proximal_forelimb_WT_H3K27me3_ChIPseq
- GSM5655989 e12.5_mouse_distal_forelimb_WT_H3K27me3_ChIPseq
- GSM5655990 e12.5_mouse_proximal_forelimb_EEDc/-_H3K27me3_ChIPseq
- GSM5655991 e12.5_mouse_distal_forelimb_EEDc/-_H3K27me3_ChIPseq
- GSM5655992 e12.5_mouse_distal_forelimb_WT_CBX2_ChIPseq
- GSM5655993 e12.5_mouse_distal_forelimb_EEDc/-_CBX2_ChIPseq
- GSM5655994 e12.5_mouse_distal_forelimb_WT_H2AK119ub_ChIPseq
- GSM5655995 e12.5_mouse_distal_forelimb_EEDc/-_H2AK119ub_ChIPseq
- GSM5655996 e12.5_mouse_distal_forelimb_WT_RYBP_ChIPseq
- GSM5655997 e12.5_mouse_distal_forelimb_EEDc/-_RYBP_ChIPseq
- GSM5655998 e12.5_mouse_INPUT (FG_CD1)
- GSM5655999 e12.5_mouse_INPUT (FG-KMI_CD1)
- GSM5656122 e12.5_mouse_distal_forelimb_WT469_RNAseq
- GSM5656123 e12.5_mouse_proximal_forelimb_WT469_RNAseq
- GSM5656124 e12.5_mouse_distal_forelimb_WT512_RNAseq
- GSM5656125 e12.5_mouse_proximal_forelimb_WT512_RNAseq
- GSM5656126 e12.5_mouse_distal_forelimb_WT514_RNAseq
- GSM5656127 e12.5_mouse_proximal_forelimb_WT514_RNAseq
- GSM5656128 e12.5_mouse_distal_forelimb_Eed427_RNAseq
- GSM5656129 e12.5_mouse_proximal_forelimb_Eed427_RNAseq
- GSM5656130 e12.5_mouse_distal_forelimb_Eed445_RNAseq
- GSM5656131 e12.5_mouse_proximal_forelimb_Eed445_RNAseq
- GSM5656132 e12.5_mouse_distal_forelimb_Eed448_RNAseq
- GSM5656133 e12.5_mouse_proximal_forelimb_Eed448_RNAseq
- GSE269318 Cancer-intrinsic Cxcl5 orchestrates global metabolic reprogramming of three dimensional cancers by upregulating Hif1α and Myc expression 31 samples shares regulating, program
- GSE283748 Skatole attenuates osteoarthritis by protecting chondrocytes and mediating macrophage repolarization through regulating the NFκB/MAPK signaling pathway and metabolic reprogramming II 10 samples shares regulating, program
- GSE310209 Opposing functions of AEBP2 isoforms fine-tune PRC2 catalytic activity 72 samples shares prc2
- GSE278724 Allosteric effectors of PRC2 synergise to restrict Polycomb domains spread 60 samples shares prc2
- GSE249591 Gene suppression by PRC2 enhances the gene inductions by Aire and the development of mimetic cell populations 572 samples shares prc2
- GSE249218 Non-Canonical PRC1.1 is required for the activity of Menin-MLL1 Inhibitors in NUP98-Rearranged AML 220 samples shares prc1
- GSE272603 DNA glycosylases Ogg1 and Mutyh mediate gene expression of PRC2 targets important for memory formation 128 samples shares prc2
- GSE297309 SKP1A-mediated degradation of PRC2 triggers activation of Polycomb-silenced gene [CUT&Tag] 108 samples shares prc2
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.