Wnt signaling dosage controlled by a Ctnnb1 enhancer balances homeostasis and tumorigenesis of intestinal epithelia
RNA-seq (gene expression) · mouse · 20 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
- 20 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
- A Ctnnb1 enhancer transcriptionally regulates Wnt signaling dosage to balance homeostasis and tumorigenesis of intestinal epitheliaeLife · 2024
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE233979_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA979138 and SRA study SRP440936. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 20 samples.
How we read this: 6 replicated groups read from 20 sample titles; they account for 20 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.
- GSM7440081 Crypt_WT_rep1 Crypt_WT
- GSM7440082 Crypt_WT_rep2 Crypt_WT
- GSM7440083 Crypt_WT_rep3 Crypt_WT
- GSM7440084 Crypt_KO_rep1 Crypt_KO
- GSM7440085 Crypt_KO_rep2 Crypt_KO
- GSM7440086 Crypt_KO_rep3 Crypt_KO
- GSM7440087 Tumor_WT_ rep1 Tumor_WT
- GSM7440088 Tumor_WT_ rep2 Tumor_WT
- GSM7440089 Tumor_WT_ rep3 Tumor_WT
- GSM7440090 Tumor_KO_ rep1 Tumor_KO
- GSM7440091 Tumor_KO_ rep2 Tumor_KO
- GSM7440092 Tumor_KO_ rep3 Tumor_KO
- GSM7440093 scRNA-seq_WT_1 scRNA-seq_WT
- GSM7440094 scRNA-seq_WT_2 scRNA-seq_WT
- GSM7440095 scRNA-seq_WT_3 scRNA-seq_WT
- GSM7440096 scRNA-seq_WT_4 scRNA-seq_WT
- GSM7440097 scRNA-seq_KO_1 scRNA-seq_KO
- GSM7440098 scRNA-seq_KO_2 scRNA-seq_KO
- GSM7440099 scRNA-seq_KO_3 scRNA-seq_KO
- GSM7440100 scRNA-seq_KO_4 scRNA-seq_KO
- GSE276270 NOTCH-driven oscillations control cell fate decisions during intestinal homeostasis 36 samples shares homeostasis, intestinal
- GSE279700 Cooperation of TRADD- and RIPK1-dependent Cell Death Pathways in Maintaining Intestinal Homeostasis [3 DPI colon] 35 samples shares homeostasis, intestinal
- GSE306906 Fosl1 is a transcriptional effector of BRAFV600E-driven intestinal tumorigenesis 27 samples shares tumorigenesis, intestinal
- GSE301459 Elucidating the impact of KRAS Gly12 mutants on homeostasis and tumorigenesis in the colonic epithelium 24 samples shares tumorigenesis, homeostasis
- GSE329264 Impact of Intestinal Propionate Metabolism on Systemic Metabolic Homeostasis 20 samples shares homeostasis, intestinal
- GSE270542 Antithrombin-binding heparan sulfate is ubiquitously expressed in epithelial cells and suppresses pancreatic tumorigenesis 18 samples shares tumorigenesis, epithelia
- GSE295548 Tumorigenic p53S Balances Aging and Tumorigenesis via Regulating DREAM/MMB and its Downstream Telomere DNA Replication Pathways 15 samples shares tumorigenesis, balances
- GSE326488 Ubiquitin-like proteins NEDD8 and SUMO2 control epithelial homeostasis, regeneration, and inflammation [RNA-Seq mouse] 14 samples shares homeostasis, epithelia
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.