GEO series

Epitranscriptomic profiling of m6A RNA modifications in THP-1 monocytic cell line.

GSE289760 Homo sapiens (human) DNA methylation 2 samples Submitted 2025/02/18 Platform GPL24676

At a glance

DNA methylation · human · 2 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 2 samples
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: M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modificationsGigaScience · 2025

Summary (written by the submitters)

Allele-specific regulatory events are essential in many fundamental biological processes. In this study, we utilized the human monocytic cell line THP-1 and performed RNA immunoprecipitation sequencing (MeRIP-seq) to explore allele-specific regulation of N6-methyladenosine (m6A) RNA modifications. Recent research highlights the importance of allele-specific regulation of m6A (ASm6A) and the need for precise detection methods to elucidate its underlying mechanisms.

Read the full summary ↓

To address limitations in current approaches, which often emphasize genetic variations rather than comprehensive regulatory mechanisms, we applied M6Allele, a meta-analysis framework based on hierarchical Bayesian models. This method enables accurate detection of ASm6A events at the peak level, providing new insights into allele-specific regulatory mechanisms of m6A modifications. Our findings from the THP-1 cell line contribute to a deeper understanding of ASm6A and its biological significance.

Published in

M6Allele: a toolkit for detection of allele-specific RNA N6-methyladenosine modifications

Zhang Y, Tang L, Zhi S et al. · GigaScience 2025 · PMID 40388309 · doi:10.1093/gigascience/giaf040

This dataset

Open GSE289760 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 GSE289760_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1224735 and SRA study SRP564344. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40388309) ↗

Samples in this study

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+ 2 more — browse all 2 samples with per-sample file links →

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