Differential 5-FU responses of crypt-derived organoids embedded in collagen versus Matrigel, and their transcriptomic comparison with villus-derived organoids
RNA-seq (gene expression) · mouse · 18 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
- 18 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
- Fetal reversion from diverse lineages sustains the intestinal stem cell pool and confers stress resilienceCommunications biology · 2026
Read the full summary ↓
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 GSE310410_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 PRJNA1365904 and SRA study SRP646677. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 18 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.
- GSM9300631 MG_Control_1 MG_Control
- GSM9300632 MG_Control_2 MG_Control
- GSM9300633 MG_Control_3 MG_Control
- GSM9300634 MG_5FU_1 MG_5FU
- GSM9300635 MG_5FU_2 MG_5FU
- GSM9300636 MG_5FU_3 MG_5FU
- GSM9300637 COL_Control_1 COL_Control
- GSM9300638 COL_Control_2 COL_Control
- GSM9300639 COL_Control_3 COL_Control
- GSM9300640 COL_5FU_1 COL_5FU
- GSM9300641 COL_5FU_2 COL_5FU
- GSM9300642 COL_5FU_3 COL_5FU
- GSM9300643 COL_cWRNE_1 COL_cWRNE
- GSM9300644 COL_cWRNE_2 COL_cWRNE
- GSM9300645 COL_cWRNE_3 COL_cWRNE
- GSM9300646 VIL_1 VIL
- GSM9300647 VIL_2 VIL
- GSM9300648 VIL_3 VIL
- GSE236765 RNA sequencing of LT-HSCs in the bone marrow from WT and Trim47-/- mice untreated or treated with 5-FU for 10 days 12 samples shares 5-fu
- GSE115706 RNAseq of motor neurons and neurons with differential vulnerability isolated from a mouse model of spinal muscular atrophy using laser capture microdissection 168 samples shares differential
- GSE267633 Differential Effects of Prenatal Alcohol Exposure in Mice on Brain Growth and Gene Expression Reveals Early Effects on Cell Cycle and Apoptosis and Delayed Effects on Metabolism in Affected Offspring 151 samples shares differential
- GSE286046 Asymmetric Histone Inheritance Regulates Differential Transcription Re-initiation and Cell Fate Decisions in Mouse Olfactory Horizontal Basal Cells 96 samples shares differential
- GSE318815 Differential sex-dependent responses of circulating steroid hormones and cortical gene expression in a preclinical traumatic brain injury model 88 samples shares differential
- GSE316055 Differential downstream signaling in microglia lacking Alzheimer’s-related TREM2 or its adaptor TYROBP/DAP12 72 samples shares differential
- GSE310453 Functional divergence of Capicua isoforms explains differential tissue vulnerability in neurological disease 70 samples shares differential
- GSE232199 Differential expression gene signature 56 samples shares differential
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.