GEO series

Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia [RNA-Seq]

GSE233977 Mus musculus (mouse) Single-cell RNA-seq 12 samples Submitted 2024/10/02 Platform GPL24247

At a glance

Single-cell RNA-seq · mouse · 12 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Mus musculus (mouse)
Samples: 12 samples
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: A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epitheliaeLife · 2024

Summary (written by the submitters)

β-catenin-dependent canonical Wnt signaling plays a plethora of roles in organ development, tissue homeostasis and cancer. Here we identified an upstream enhancer of Ctnnb1 - ieCtnnb1 - that controls intestinal homeostasis. ieCtnnb1 is specifically active in crypts of small and large intestines. Single-cell sequencing revealed that ieCtnnb1 knockout (ieCtnnb1KO) biased epithelial composition and functions of small intestinal crypts – leaning toward absorptive functions at the expense of secretive roles.

Read the full summary ↓

Deletion of ieCtnnb1 hampered epithelial turnovers in physiologic and regenerative conditions. In contrast, deletion of ieCtnnb1 prevents occurrence and progression of Wnt/β-catenin driving colorectal cancers. The human ieCTNNB1 specifically drives reporter in intestinal crypts and contains a SNP that is associated with CTNNB1 expression levels in human gastrointestinal epithelia. The enhancer activity of ieCTNNB1 in colorectal cancer tissues is higher than that in adjacent normal tissues and positively correlates with CTNNB1 expression levels. Key trans-factors that bind to ieCTNNB1 and regulate CTNNB1 transcription were identified. Together, these findings revealed an enhancer-dependent mechanism that controls the dosage of Wnt signaling, hence homeostasis of intestinal epithelia.

Published in

A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epithelia

Hua X, Zhao C, Tian J et al. · eLife 2024 · PMID 39320349 · doi:10.7554/eLife.98238

This dataset

Open GSE233977 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 GSE233977_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 PRJNA979140 and SRA study SRP440936. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39320349) ↗

Samples in this study

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

Datasets on a similar topic

GSE233979 Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia 20 samples shares ctnnb1, tumorigenesis, homeostasis, controlled, intestinal, epithelia, enhancer, balances
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GSE301459 Elucidating the impact of KRAS Gly12 mutants on homeostasis and tumorigenesis in the colonic epithelium 24 samples shares tumorigenesis, homeostasis
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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.