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Single cell discovery of m6A RNA modifications in the hippocampus

GSE240863 Homo sapiens (human) Single-cell RNA-seq 43 samples Submitted 2024/05/07 Platform GPL24676Platform GPL24247
At a glance

Single-cell RNA-seq · human · 43 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism
Homo sapiens (human)
Samples
43 samples: 13 conditions, mostly in triplicateGroups 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
Single-cell discovery of m(6)A RNA modifications in the hippocampusGenome research · 2024
Summary (written by the submitters)
N6-methyladenosine (m6A) is a prevalent and highly regulated RNA modification essential for RNA metabolism and normal brain function. It is particularly important in the hippocampus, where m6A is implicated in neurogenesis and learning. Although extensively studied, its presence and impact in specific cell types remain poorly understood. We investigated m6A in the hippocampus at the single-cell level, revealing a comprehensive landscape of m6A modifications within individual cells.
Published in
Single-cell discovery of m(6)A RNA modifications in the hippocampus
Feng S, Tellaetxe-Abete M, Zhang Y et al. · Genome research 2024 · PMID 39009472 · doi:10.1101/gr.278424.123
This dataset
Open GSE240863 in finder → Find more 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 GSE240863_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1005593 and SRA study SRP455180. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39009472) ↗
Study design
13 conditions, mostly in triplicate
Hippocampus, m6A RIP-input, ×3 Hippocampus, m6A RIP-pulldown, ×3 Bulk, HEK293T, APOBEC1-E, ×3 Bulk, HEK293T, E-APOBEC1, ×3 Bulk, HEK293T, E-Mut, ×3 Bulk, HEK293T, E-YTH, ×3 Bulk, HEK293T, Mock, ×3 Bulk, HEK293T, Mut-E, ×3 +9 more

Supports a between-group comparison across 39 samples.

How we read this: 13 replicated groups read from 43 sample titles; they account for 39 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

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