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MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons. [CUT&Tag]

GSE247071 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 49 samples Submitted 2024/04/26 Platform GPL20301
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 49 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
49 samples: 13 conditions, mostly in triplicateGroups 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
MECP2 directly interacts with RNA polymerase II to modulate transcription in human neuronsNeuron · 2024
Summary (written by the submitters)
Mutations in the methyl-DNA-binding protein MECP2 cause the neurodevelopmental disorder Rett syndrome (RTT). How MECP2 contributes to transcriptional regulation in normal and disease states is unresolved; it has been reported to be an activator and a repressor. We describe here the first integrated CUT&Tag, transcriptome, and proteome analyses using human neurons with wild-type and mutant MECP2 molecules.
Read the full summary ↓
MECP2 occupies CpG-rich promoter-proximal regions in over four thousand genes in human neurons, including a plethora of autism risk genes, together with RNA polymerase II (Pol II). MECP2 directly interacts with Pol II, and genes occupied by both proteins showed reduced expression in neurons with MECP2 patient mutations. We conclude that MECP2 acts as a positive cofactor for Pol II gene expression at many neuronal genes that harbor CpG-islands in promoter-proximal regions, and that RTT is due, in part, to the loss of gene activity at these genes in neurons.
Published in
MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons
Liu Y, Flamier A, Bell GW et al. · Neuron 2024 · PMID 38697112 · doi:10.1016/j.neuron.2024.04.007
This dataset
Open GSE247071 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE247071_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA1036163 and SRA study SRP470346. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38697112) ↗
Study design
13 conditions, mostly in triplicate
WT_H3K9me3 ×4 WT_IgG ×4 KO_GFP_ab2 ×3 R133C_GFP ×3 R133C_pol2 ×3 R168X_GFP ×3 R168X_pol2 ×3 R270X_GFP ×3 +13 more

Supports a between-group comparison across 41 samples.

How we read this: 13 replicated groups read from 49 sample titles; they account for 41 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.

Samples in this study

+ 9 more — browse all 49 samples with per-sample file links →

Datasets on a similar topic

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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