GEO series

MECP2 directly interacts with RNA polymerase II to modulate transcription in human neurons [RNA-Seq]

GSE230714 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/04/26 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 12 samples: 3 × MECP2.KO vs 3 × MECP2.R133C vs 3 × MECP2.R168X vs 3 × MECP2.WTGroups 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 GSE230714 in finder → Find more human RNA-seq 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 GSE230714_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA962446 and SRA study SRP434807. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38697112) ↗

Study design

3 × MECP2.KO vs 3 × MECP2.R133C vs 3 × MECP2.R168X vs 3 × MECP2.WT

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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

GSM7232983 MECP2.KO.rep1 MECP2.KO
GSM7232984 MECP2.KO.rep2 MECP2.KO
GSM7232985 MECP2.KO.rep3 MECP2.KO
GSM7232986 MECP2.R133C.rep1 MECP2.R133C
GSM7232987 MECP2.R133C.rep2 MECP2.R133C
GSM7232988 MECP2.R133C.rep3 MECP2.R133C
GSM7232989 MECP2.R168X.rep1 MECP2.R168X
GSM7232990 MECP2.R168X.rep2 MECP2.R168X
GSM7232991 MECP2.R168X.rep3 MECP2.R168X
GSM7232992 MECP2.WT.rep1 MECP2.WT
GSM7232993 MECP2.WT.rep2 MECP2.WT
GSM7232994 MECP2.WT.rep3 MECP2.WT

Datasets on a similar topic

GSE269826 Conserved patterns of transcriptional dysregulation, heterogeneity and cell states in clear cell kidney cancer [scRNA-seq] 79 samples shares transcription, rna-seq
GSE325391 Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer’s disease, and cognitive resilience 27 samples shares transcription, neurons
GSE189357 Spatiotemporal transcriptional atlas of lung adenocarcinoma from adenocarcinoma in situ to invasive carcinoma [scRNA-seq] 9 samples shares transcription, rna-seq
GSE318861 Quantitative analysis of Tat-dependent and host-driven HIV transcription by ChIP-seq and RNA-seq 52 samples shares transcription, rna-seq
GSE268177 Modulating alternative splicing of MECP2: A potential therapeutic strategy for Rett syndrome 93 samples shares mecp2
GSE314310 Cardiopedia-Ligand: a Ligand Stimulation Atlas for Cardiac Function and Transcriptional Response 468 samples shares transcription
GSE271676 Spatial Transcriptional Landscape of Human Heart Failure 178 samples shares transcription
GSE274546 The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X] 121 samples shares transcription

Search all human RNA-seq datasets in GEO →

Share this dataset

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.