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m6A modification governs the stability of both methylated and unmethylated mRNA isoforms across the transcriptome

GSE219125 Homo sapiens (human) RNA-seq (gene expression) 162 samples Submitted 2025/02/01 Platform GPL20301Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 162 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
162 samples: 60 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.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE219125 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 GSE219125_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 PRJNA907064 and SRA study SRP331939. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
60 conditions, mostly in duplicate
Input_DF2 siRNA # ×4 m6A-IP_DF2 siRNA # ×4 Input_control ×3 m6A-IP_control ×3 Ctrl siRNA_INPUT_0h ×2 Ctrl siRNA_INPUT_0.5h ×2 Ctrl siRNA_INPUT_1h ×2 Ctrl siRNA_INPUT_2h ×2 +88 more

Supports a between-group comparison across 126 samples.

How we read this: 60 replicated groups read from 162 sample titles; they account for 126 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

+ 122 more — browse all 162 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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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.