Loss of METTL3 potentiates transposable element expression and drives inflammation-induced cell plasticity in the mammary epithelium
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 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
- Homo sapiens (human)
- 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.
- Paper
- METTL3-dependent m6A RNA methylation suppresses aberrant mammary epithelial differentiation and neoplastic transformationProceedings of the National Academy of Sciences of the United States of America · 2025
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 GSE281124_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 PRJNA1182333 and SRA study SRP542697. 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.
- GSM8607490 MCF10A cells, sg control, rep1 (ATAC-seq)
- GSM8607491 MCF10A cells, sgMETTL3-2, rep1 (ATAC-seq)
- GSM8607492 MCF10A cells, sgMETTL3-4, rep1 (ATAC-seq)
- GSM8607493 MCF10A cells, sg control, rep2 (ATAC-seq)
- GSM8607494 MCF10A cells, sgMETTL3-2, rep2 (ATAC-seq)
- GSM8607495 MCF10A cells, sgMETTL3-4, rep2 (ATAC-seq)
- GSM8607496 MCF10A cells, sg control, rep1 (ChIP-seq)
- GSM8607497 MCF10A cells, sgMETTL3-2, rep1 (ChIP-seq)
- GSM8607498 MCF10A cells, sgMETTL3-4, rep1 (ChIP-seq)
- GSM8607499 MCF10A cells, sg control, rep2 (ChIP-seq)
- GSM8607500 MCF10A cells, sgMETTL3-2, rep2 (ChIP-seq)
- GSM8607501 MCF10A cells, sgMETTL3-4, rep2 (ChIP-seq)
- GSM8607502 MCF10A cells, sg control, rep1 (RNA-seq)
- GSM8607503 MCF10A cells, sg control, rep2 (RNA-seq)
- GSM8607504 MCF10A cells, sg control, rep3 (RNA-seq)
- GSM8607505 MCF10A cells, sgMETTL3-2, rep1 (RNA-seq)
- GSM8607506 MCF10A cells, sgMETTL3-2, rep2 (RNA-seq)
- GSM8607507 MCF10A cells, sgMETTL3-2, rep3 (RNA-seq)
- GSM8607508 MCF10A cells, sgMETTL3-4, rep1 (RNA-seq)
- GSM8607509 MCF10A cells, sgMETTL3-4, rep2 (RNA-seq)
- GSM8607510 MCF10A cells, sgMETTL3-4, rep3 (RNA-seq)
- GSM8607511 normal breast organoid, sgAAVS1 (scRNA-seq)
- GSM8607512 normal breast organoid, sgMETTL3-2 (scRNA-seq)
- GSM8607513 normal breast organoid, sgMETTL3-4 (scRNA-seq)
- GSE275738 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells 72 samples shares mettl3, transposable, element
- GSE274217 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [RNA-Seq] 28 samples shares mettl3, transposable, element
- GSE275737 METTL3-dependent m6A RNA methylation represses transposable elements derived enhancers to suppress naïve pluripotency in human pluripotent stem cells [ChIP-Seq] 21 samples shares mettl3, transposable, element
- GSE296929 E2F4/SETD1A axis-mediated METTL3 methylation promotes tumor immune evasion through impeding endogenous retroelements expression 18 samples shares mettl3, element
- GSE292478 Hominoid-specific transposable elements reshaped neural crest migration in craniofacial development 17 samples shares transposable, element
- GSE234237 Transposable Elements Shape Stemness in Normal and Leukemic Hematopoiesis 215 samples shares transposable, element
- GSE270454 Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer’s disease 135 samples shares transposable, element
- GSE254244 Cancer cell type-specific derepression of transposable elements by inhibition of chromatin modifier enzymes 112 samples shares transposable, element
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.