G-quadruplex folding in Xist RNA antagonizes PRC2 activity for step-wise regulation of X-chromosome inactivation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 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
- Mus musculus (mouse)
- Samples
- 36 samples: 12 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
- G-quadruplex folding in Xist RNA antagonizes PRC2 activity for stepwise regulation of X chromosome inactivationMolecular cell · 2024
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 GSE219083_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 PRJNA906999 and SRA study SRP410676. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 36 sample titles; they account for 24 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.
- GSM7946720 DMS seq WT D0 rep1 DMS seq WT D0
- GSM7946721 DMS seq WT D0 rep2 DMS seq WT D0
- GSM7946722 DMS seq WT D3 rep1 DMS seq WT D3
- GSM7946723 DMS seq WT D3 rep2 DMS seq WT D3
- GSM7946724 DMS seq WT D7 rep1 DMS seq WT D7
- GSM7946725 DMS seq WT D7 rep2 DMS seq WT D7
- GSM7946789 WT_D7_Xist_CHART rep1 WT_D7_Xist_CHART
- GSM7946790 3rG4_cl5_D7_Xist_CHART rep1 3rG4_cl5_D7_Xist_CHART
- GSM7946791 3rG4_cl6_D7_Xist_CHART rep1 3rG4_cl6_D7_Xist_CHART
- GSM7946792 WT_D7_Xist_CHART rep2 WT_D7_Xist_CHART
- GSM7946793 3rG4_cl5_D7_Xist_CHART rep2 3rG4_cl5_D7_Xist_CHART
- GSM7946794 3rG4_cl6_D7_Xist_CHART rep2 3rG4_cl6_D7_Xist_CHART
- GSM7946795 WT_D7_Xist_CHART rep1 input
- GSM7946796 3rG4_cl5_D7_Xist_CHART rep1 input
- GSM7946797 3rG4_cl6_D7_Xist_CHART rep1 input
- GSM7946798 WT_D7_Xist_CHART rep2 input
- GSM7946799 3rG4_cl5_D7_Xist_CHART rep2 input
- GSM7946800 3rG4_cl6_D7_Xist_CHART rep2 input
- GSM7946821 WT(3rG4) D7 RNA rep1 WT(3rG4) D7 RNA
- GSM7946822 3rG4 cl5 D7 RNA rep1 3rG4 cl5 D7 RNA
- GSM7946823 3rG4 cl6 D7_RNA rep1 3rG4 cl6 D7_RNA
- GSM7946824 WT(3rG4) D7 RNA rep2 WT(3rG4) D7 RNA
- GSM7946825 3rG4 cl5 D7 RNA rep2 3rG4 cl5 D7 RNA
- GSM7946826 3rG4 cl6 D7_RNA rep2 3rG4 cl6 D7_RNA
- GSM7946833 WT(3rG4) K27me3 rep1 WT(3rG4) K27me3
- GSM7946834 3rG4 cl5 k27me3 rep1 3rG4 cl5 k27me3
- GSM7946835 3rG4 cl6 k27me3 rep1 3rG4 cl6 k27me3
- GSM7946836 WT(3rG4) K27me3 rep2 WT(3rG4) K27me3
- GSM7946837 3rG4 cl5 k27me3 rep2 3rG4 cl5 k27me3
- GSM7946838 3rG4 cl6 k27me3 rep2 3rG4 cl6 k27me3
- GSM7946839 WT(3rG4) K27me3 rep1 input
- GSM7946840 3rG4 cl5 k27me3 rep1 input
- GSM7946841 3rG4 cl6 k27me3 rep1 input
- GSM7946842 WT(3rG4) K27me3 rep2 input
- GSM7946843 3rG4 cl5 k27me3 rep2 input
- GSM7946844 3rG4 cl6 k27me3 rep2 input
- GSE223666 Alternative splicing decouples local from global PRC2 activity 87 samples shares prc2, activity
- GSE310209 Opposing functions of AEBP2 isoforms fine-tune PRC2 catalytic activity 72 samples shares prc2, activity
- GSE239636 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation [CUT&RUN] 60 samples shares prc2, activity
- GSE306783 EPOP and MTF2 Activate PRC2 Activity through DNA-sequence specificity 34 samples shares prc2, activity
- GSE286459 The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [delSBD-ChIP-Rx] 18 samples shares prc2, activity
- GSE257545 Top2a Differentially Modulates Promoter Activity in Embryonic Stem Cells via Trim28 Recruitment and PRC2 Displacement [ChIP-Seq] 16 samples shares prc2, activity
- GSE286457 The conserved N-terminal SANT1-binding domain (SBD) of EZH2 Regulates PRC2 Activity [MTF2-JARID2] 15 samples shares prc2, activity
- GSE239632 Cancer-associated Histone H3 N-terminal arginine mutations disrupt PRC2 activity and impair differentiation [RNA-Seq] 15 samples shares prc2, activity
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.