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Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney

GSE243871 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2024/05/27 Platform GPL30172Platform GPL21697
At a glance

Single-cell RNA-seq · human · 28 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)
Topic
Wilms tumourThis series is part of our curated briefing on it.
Samples
28 samples: 6 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 multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscapeNature 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
Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape
Song L, Li Q, Xia L et al. · Nature communications 2024 · PMID 39009564 · doi:10.1038/s41467-024-50171-w
This dataset
Open GSE243871 in finder → Find more ChIP / ATAC / CUT&Tag datasets → Wilms tumour landscape →
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 GSE243871_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 PRJNA1020190 and SRA study SRP462754. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39009564) ↗
Study design
6 conditions, mostly in triplicate
HEK293 cells, ENL-WT, DMSO, ×3 HEK293 cells, ENL-WT, TDI-11055, ×3 HEK293 cells, ENL-T1, DMSO, ×3 HEK293 cells, ENL-T1, TDI-11055, ×3 HEK293 cells, ENL-T2, DMSO, ×3 HEK293 cells, ENL-T2, TDI-11055, ×3 HEK293 cells, Flag-ENL-WT, DMSO, ChIP-seq ×1 HEK293 cells, Flag-ENL-WT, TDI-11055, ChIP-seq ×1 +8 more

Supports a between-group comparison across 18 samples.

How we read this: 6 replicated groups read from 28 sample titles; they account for 18 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
More Wilms tumour datasets

Search all ChIP / ATAC / CUT&Tag 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.