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IGF2BP3 promotes mRNA degradation through internal m7G modification

GSE241222 Homo sapiens (human) DNA methylation 52 samples Submitted 2024/07/13 Platform GPL24676
At a glance

DNA methylation · human · 52 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Samples
52 samples: 24 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
IGF2BP3 promotes mRNA degradation through internal m(7)G modificationNature communications · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
IGF2BP3 promotes mRNA degradation through internal m(7)G modification
Liu C, Dou X, Zhao Y et al. · Nature communications 2024 · PMID 39198433 · doi:10.1038/s41467-024-51634-w
This dataset
Open GSE241222 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 GSE241222_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 PRJNA1006739 and SRA study SRP455771. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39198433) ↗
Study design
24 conditions, mostly in duplicate
HepG2 siControl Input ×3 HepG2 siControl RPF ×3 HepG2 siIGF2BP3 Input ×3 HepG2 siIGF2BP3 RPF ×3 HepG2 siControl 0h ×2 HepG2 siControl 3h ×2 HepG2 siControl 6h ×2 HepG2 siIGF2BP1 0h ×2 +16 more

Supports a between-group comparison across 52 samples.

How we read this: 24 replicated groups read from 52 sample titles; they account for 52 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

+ 12 more — browse all 52 samples with per-sample file links →

Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

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