An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formation (RNA-seq)
RNA-seq (gene expression) · mouse · 44 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
- 44 samples: 15 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
- An extracellular matrix niche secreted by epithelial cells drives intestinal organoid formationDevelopmental cell · 2025
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 GSE293374_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 PRJNA1244295 and SRA study SRP575371. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 44 samples.
How we read this: 15 replicated groups read from 44 sample titles; they account for 44 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.
- GSM8881096 Mat, D04, ENRCV, Rep1 Mat, D04, ENRCV,
- GSM8881097 Mat, D04, ENRCV, Rep2 Mat, D04, ENRCV,
- GSM8881098 Mat, D04, ENRCV, Rep3 Mat, D04, ENRCV,
- GSM8881099 Mat, D06, ENRCD, Rep1 Mat, D06, ENRCD,
- GSM8881100 Mat, D06, ENRCD, Rep2 Mat, D06, ENRCD,
- GSM8881101 Mat, D06, ENRCD, Rep3 Mat, D06, ENRCD,
- GSM8881102 Mat, D06, ENRCV, Rep1 Mat, D06, ENRCV,
- GSM8881103 Mat, D06, ENRCV, Rep2 Mat, D06, ENRCV,
- GSM8881104 Mat, D06, ENRCV, Rep3 Mat, D06, ENRCV,
- GSM8881105 Mat, D06, ENRD, Rep1 Mat, D06, ENRD,
- GSM8881106 Mat, D06, ENRD, Rep2 Mat, D06, ENRD,
- GSM8881107 Mat, D06, ENRD, Rep3 Mat, D06, ENRD,
- GSM8881108 Mat, D06, ENR, Rep1 Mat, D06, ENR,
- GSM8881109 Mat, D06, ENR, Rep2 Mat, D06, ENR,
- GSM8881110 Mat, D06, ENR, Rep3 Mat, D06, ENR,
- GSM8881111 PegLam, D04, ENRCV, Rep1 PegLam, D04, ENRCV,
- GSM8881112 PegLam, D04, ENRCV, Rep2 PegLam, D04, ENRCV,
- GSM8881113 PegLam, D04, ENRCV, Rep3 PegLam, D04, ENRCV,
- GSM8881114 PegLam, D06, ENRCD, Rep1 PegLam, D06, ENRCD,
- GSM8881115 PegLam, D06, ENRCD, Rep2 PegLam, D06, ENRCD,
- GSM8881116 PegLam, D06, ENRCD, Rep3 PegLam, D06, ENRCD,
- GSM8881117 PegLam, D06, ENRCV, Rep1 PegLam, D06, ENRCV,
- GSM8881118 PegLam, D06, ENRCV, Rep2 PegLam, D06, ENRCV,
- GSM8881119 PegLam, D06, ENRCV, Rep3 PegLam, D06, ENRCV,
- GSM8881120 PegLam, D06, ENRD, Rep1 PegLam, D06, ENRD,
- GSM8881121 PegLam, D06, ENRD, Rep2 PegLam, D06, ENRD,
- GSM8881122 PegLam, D06, ENRD, Rep3 PegLam, D06, ENRD,
- GSM8881123 PegLam, D06, ENR, Rep1 PegLam, D06, ENR,
- GSM8881124 PegLam, D06, ENR, Rep2 PegLam, D06, ENR,
- GSM8881125 PegLam, D06, ENR, Rep3 PegLam, D06, ENR,
- GSM8881126 PegN, D04, ENRCV, Rep1 PegN, D04, ENRCV,
- GSM8881127 PegN, D04, ENRCV, Rep2 PegN, D04, ENRCV,
- GSM8881128 PegN, D04, ENRCV, Rep3 PegN, D04, ENRCV,
- GSM8881129 PegN, D06, ENRCD, Rep1 PegN, D06, ENRCD,
- GSM8881130 PegN, D06, ENRCD, Rep2 PegN, D06, ENRCD,
- GSM8881131 PegN, D06, ENRCD, Rep3 PegN, D06, ENRCD,
- GSM8881132 PegN, D06, ENRCV, Rep1 PegN, D06, ENRCV,
- GSM8881133 PegN, D06, ENRCV, Rep2 PegN, D06, ENRCV,
- GSM8881134 PegN, D06, ENRCV, Rep3 PegN, D06, ENRCV,
- GSM8881135 PegN, D06, ENRD, Rep1 PegN, D06, ENRD,
+ 4 more — browse all 44 samples with per-sample file links →
- GSE300722 Organoid modeling of lung branching morphogenesis and epithelial lineage specification [RNA-Seq] 40 samples shares epithelial, organoid, rna-seq
- GSE293383 Viscoelastic Extracellular Matrix Enhances Epigenetic Remodeling and Cellular Plasticity [RNA-seq] 12 samples shares extracellular, rna-seq, matrix
- GSE329635 Single-cell RNA sequencing of small intestinal organoid self-organization [scRNA-Seq] 10 samples shares intestinal, organoid, rna-seq
- GSE295428 Spaceflight induces systemic effects on extracellular matrix and immune system in different age-stages 229 samples shares extracellular, matrix
- GSE205410 Multiple subpopulations in medullary thymic epithelial cells are regulated by Aire with distinctive modes of gene regulations [bulkRNA-seq] 47 samples shares epithelial, rna-seq
- GSE248585 A conserved epithelial wound-like transcriptional program driven by FOSL1 underlies malignant progression of pancreatic ductal adenocarcinoma (ssRNA-Seq) 46 samples shares epithelial, rna-seq
- GSE289885 Hybrid hydrogel–extracellular matrix scaffolds identify biochemical and mechanical signatures of cardiac ageing 29 samples shares extracellular, matrix
- GSE283495 Intestinal epithelial cell diversity and function in respect to age, anatomical localization, and microbial exposure - the global transcriptome 29 samples shares epithelial, intestinal
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.