GEO series

Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control [RNA-seq]

GSE266256 Mus musculus (mouse) RNA-seq (gene expression) 32 samples Submitted 2025/02/20 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 32 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: Mus musculus (mouse)
Samples: 32 samples: 11 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: Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney developmentNature communications · 2025

Summary (written by the submitters)

Hotspot gain-of-function mutations in the YEATS domain of the histone reader protein ENL have been identified in Wilms’ tumor. To investigate the pathogenic role of these cancer-associated ENL mutations in kidney development and tumorigenesis in vivo, we generated conditional knock-in mouse models mimicking patient-derived ENL YEATS mutations.

Read the full summary ↓

Mice with heterozygous expression of ENLT mutants in either Six2+ nephrogenic or Foxd1+ stromal lineage exhibit severe yet distinct defects in kidney development, both resulting in neonatal lethality. The Six2-ENLT mutant kidney rudiments display compromised cap mesenchyme, scant proximal tubules and cystic glomeruli, indicative of premature commitment and differentiation blockade during nephrogenesis. Bulk and spatial transcriptomic analyses uncover aberrant activation of Hox genes and genes involved in cell fate commitment, especially the Wnt signaling pathway, in ENLT mutant-expressing nephrogenic cells. In contrast, the Foxd1-ENLT mutant kidneys exhibit expansion in renal capsule and cap mesenchyme, accompanied with dysregulation of stromal genes involved in nephrogenesis and stroma-nephron crosstalk. Collectively, our study sheds lights on how ENL YEATS domain mutations impede nephrogenesis through different pathways in nephrogenic and stromal lineages, paving the way for further investigations into their roles in tumorigenesis.

Published in

Expression of ENL YEATS domain tumor mutations in nephrogenic or stromal lineage impairs kidney development

Xue Z, Xuan H, Lau K et al. · Nature communications 2025 · PMID 40087269 · doi:10.1038/s41467-025-57926-z

This dataset

Open GSE266256 in finder → Find more mouse 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 GSE266256_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 PRJNA1106455 and SRA study SRP504971. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40087269) ↗

Study design

11 conditions, mostly in triplicate

Foxd1_sort_E185_WT ×4 Foxd1_sort_E185_T1 ×4 Foxd1_E185_T1 ×3 Foxd1_E185_WT ×3 Six2_sort_E145_T1 ×3 Six2_sort_E145_WT ×3 Six2_sort_E185_T1 ×3 Six2_sort_E185_WT ×3 +3 more

Supports a between-group comparison across 32 samples.

How we read this: 11 replicated groups read from 32 sample titles; they account for 32 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

GSM8243870 Foxd1_E185_T1_rep1 Foxd1_E185_T1
GSM8243871 Foxd1_E185_T1_rep2 Foxd1_E185_T1
GSM8243872 Foxd1_E185_T1_rep3 Foxd1_E185_T1
GSM8243873 Foxd1_E185_WT_rep1 Foxd1_E185_WT
GSM8243874 Foxd1_E185_WT_rep2 Foxd1_E185_WT
GSM8243875 Foxd1_E185_WT_rep3 Foxd1_E185_WT
GSM8243876 Six2_E185_T1_rep1 Six2_E185_T1
GSM8243877 Six2_E185_T1_rep2 Six2_E185_T1
GSM8243878 Six2_E185_T3_rep1 Six2_E185_T3
GSM8243879 Six2_E185_T3_rep2 Six2_E185_T3
GSM8243880 Six2_E185_WT_rep1 Six2_E185_WT
GSM8243881 Six2_E185_WT_rep2 Six2_E185_WT
GSM8243882 Six2_sort_E145_T1_rep1 Six2_sort_E145_T1
GSM8243883 Six2_sort_E145_T1_rep2 Six2_sort_E145_T1
GSM8243884 Six2_sort_E145_T1_rep3 Six2_sort_E145_T1
GSM8243885 Six2_sort_E145_WT_rep1 Six2_sort_E145_WT
GSM8243886 Six2_sort_E145_WT_rep2 Six2_sort_E145_WT
GSM8243887 Six2_sort_E145_WT_rep3 Six2_sort_E145_WT
GSM8243888 Six2_sort_E185_T1_rep1 Six2_sort_E185_T1
GSM8243889 Six2_sort_E185_T1_rep2 Six2_sort_E185_T1
GSM8243890 Six2_sort_E185_T1_rep3 Six2_sort_E185_T1
GSM8243891 Six2_sort_E185_WT_rep1 Six2_sort_E185_WT
GSM8243892 Six2_sort_E185_WT_rep2 Six2_sort_E185_WT
GSM8243893 Six2_sort_E185_WT_rep3 Six2_sort_E185_WT
GSM8761524 Foxd1_sort_E185_WT_rep1 Foxd1_sort_E185_WT
GSM8761525 Foxd1_sort_E185_WT_rep2 Foxd1_sort_E185_WT
GSM8761526 Foxd1_sort_E185_WT_rep3 Foxd1_sort_E185_WT
GSM8761527 Foxd1_sort_E185_WT_rep4 Foxd1_sort_E185_WT
GSM8761528 Foxd1_sort_E185_T1_rep1 Foxd1_sort_E185_T1
GSM8761529 Foxd1_sort_E185_T1_rep2 Foxd1_sort_E185_T1
GSM8761530 Foxd1_sort_E185_T1_rep3 Foxd1_sort_E185_T1
GSM8761531 Foxd1_sort_E185_T1_rep4 Foxd1_sort_E185_T1

Datasets on a similar topic

GSE283435 Gain-of-function ENL YEATS domain mutations impede nephrogenesis through gene expression control 34 samples shares yeats, enl, gain-of-function, nephrogenesis, mutations, control, domain
GSE303246 The MLLT3 YEATS domain is a dual reader of histone marks (H3K9/18/27ac/cr) and ncRNA (7SK), linking epigenetic and RNA signaling to regulate hematopoiesis [RNA-Seq] 6 samples shares yeats, rna-seq, domain
GSE239469 Condensate-promoting ENL mutation induces tumorigenesis via chromatin remodeling [RNA-seq] 28 samples shares enl, rna-seq
GSE293107 SKIDA1 transiently sustains MLL::ENL-Expressing hematopoietic progenitors during neonatal stages and promotes B-lineage priming [RNA-Seq] 24 samples shares enl, rna-seq
GSE291040 Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 [Bulk RNA-seq] 24 samples shares enl, rna-seq
GSE291037 Heritable fetal protection against MLL::ENL-driven leukemogenesis depends on MLL3 [scRNA-seq] 14 samples shares enl, rna-seq
GSE229484 Gene expression profiling of ST-HSCs and MPP2 cells conditionally expressing MLL-ENL by RNA-seq 4 samples shares enl, rna-seq
GSE243870 Single-Cell multi-omics reveals disrupted gene regulatory landscape and cell differentiation by Wilms tumor-associated ENL mutation in the developing kidney (scRNA-Seq) 3 samples shares enl, rna-seq

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.