Exploring the Role of DNMT1 in RNA m⁵C Methylation (eCLIPseq II)
DNA methylation · human · 11 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Homo sapiens (human)
- Samples
- 11 samples: 5 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
- DNA methyltransferase 1 modulates mitochondrial function through bridging m(5)C RNA methylationMolecular cell · 2025
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 GSE290473_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA1228131 and SRA study SRP566262. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 5 replicated groups read from 11 sample titles; they account for 10 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.
- GSM8815038 eCLIP-seq NSUN2 IP rep1 eCLIP-seq NSUN2 IP
- GSM8815039 eCLIP-seq NSUN2 IP rep2 eCLIP-seq NSUN2 IP
- GSM8815040 eCLIP-seq NSUN2 Input rep1 eCLIP-seq NSUN2 Input
- GSM8815041 eCLIP-seq NSUN2 Input rep2 eCLIP-seq NSUN2 Input
- GSM8815042 eCLIP-seq DNMT1 IP HeLa rep1 eCLIP-seq DNMT1 IP HeLa
- GSM8815043 eCLIP-seq DNMT1 IP HeLa rep2 eCLIP-seq DNMT1 IP HeLa
- GSM8815044 eCLIP-seq DNMT1 Input HeLa rep1 eCLIP-seq DNMT1 Input H…
- GSM8815045 eCLIP-seq DNMT1 Input HeLa rep2 eCLIP-seq DNMT1 Input H…
- GSM8815046 eCLIP-seq DNMT1 IP 293T rep1 eCLIP-seq DNMT1 IP 293T
- GSM8815047 eCLIP-seq DNMT1 IP 293T rep2 eCLIP-seq DNMT1 IP 293T
- GSM8815048 eCLIP-seq DNMT1 Input 293T
- GSE337276 DNA methylation maintenance by DNMT1 is essential for human trophoblast stem cell homeostasis and differentiation [RNA-seq] 15 samples shares dnmt1, methylation
- GSE233726 Exploring DNMT1 genome binding under homeostatic and hypomethylating conditions [ChIP-seq] 12 samples shares dnmt1, exploring
- GSE284387 DNMT1 RFTS mutation alters RNA splicing and drives neurodegeneration via its RNA-binding function [RNA-Seq] 26 samples shares dnmt1
- GSE329512 SUMOylation enhances DNMT1 function to repress mega-intergenic RNAs and viral mimicry 19 samples shares dnmt1
- GSE329305 SUMOylation enhances DNMT1 function to repress mega-intergenic RNAs and viral mimicry [ChIP_WT-vs-CW-dTAG] 14 samples shares dnmt1
- GSE298941 Discovery of a Novel DNMT1 Inhibitor with Improved Efficacy in Treating β-Thalassemia [ATAC-seq] 10 samples shares dnmt1
- GSE256353 Upregulated cholesterol biosynthesis facilitates the survival of methylation-retaining AML cells following decitabine treatment [single_colony_TEM-Seq] 1728 samples shares methylation
- GSE74193 Mapping DNA methylation across development, genotype, and schizophrenia in the human frontal cortex 675 samples shares methylation
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.