Bulk RNA-seq of colonic epithelial stem cell-derived organoids from healthy epithelial HO-1 knockout and control mice exposed to hemin vs vehicle
RNA-seq (gene expression) · mouse · 12 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
- 12 samples: 3 × Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, vs 3 × Epithelial organoid from Hmox1 fl/fl mice, hemin treated, vs 3 × Epithelial organoid from Hmox1 KO mice, vehicle treated, vs 3 × Epithelial organoid from Hmox1 KO mice, hemin treated,Groups 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
- Epithelial HO-1 regulates iron availability and promotes colonic tumorigenesis in a context-dependent mannerJCI insight · 2026
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 GSE312912_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 PRJNA1377590 and SRA study SRP653447. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM9356931 Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 1 Epithelial organoid fro…
- GSM9356932 Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 2 Epithelial organoid fro…
- GSM9356933 Epithelial organoid from Hmox1 fl/fl mice, vehicle treated, 3 Epithelial organoid fro…
- GSM9356934 Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 1 Epithelial organoid fro…
- GSM9356935 Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 2 Epithelial organoid fro…
- GSM9356936 Epithelial organoid from Hmox1 fl/fl mice, hemin treated, 3 Epithelial organoid fro…
- GSM9356937 Epithelial organoid from Hmox1 KO mice, vehicle treated, 1 Epithelial organoid fro…
- GSM9356938 Epithelial organoid from Hmox1 KO mice, vehicle treated, 2 Epithelial organoid fro…
- GSM9356939 Epithelial organoid from Hmox1 KO mice, vehicle treated, 3 Epithelial organoid fro…
- GSM9356940 Epithelial organoid from Hmox1 KO mice, hemin treated, 1 Epithelial organoid fro…
- GSM9356941 Epithelial organoid from Hmox1 KO mice, hemin treated, 2 Epithelial organoid fro…
- GSM9356942 Epithelial organoid from Hmox1 KO mice, hemin treated, 3 Epithelial organoid fro…
- GSE263080 RNA-sea of Smad4 wild-type or Smad4 knockout KPC PDAC organoids from monocultures or co-cultures with pancreatic stellate cells and RNA-seq of flow-sorted PSCs from the same co-cultures. 44 samples shares organoids, knockout, rna-seq
- GSE269973 Signaling basis of gastric epithelial cell differentiation revealed by human and mouse organoids [RNA-Seq] 32 samples shares epithelial, organoids, rna-seq
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares organoids, knockout, rna-seq
- GSE307773 Oncogenic MAPK signalling induces epithelial cell state change and therapeutic resistance in vivo [RNA-Seq] 175 samples shares epithelial, rna-seq
- 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
- GSE300722 Organoid modeling of lung branching morphogenesis and epithelial lineage specification [RNA-Seq] 40 samples shares epithelial, rna-seq
- GSE253461 Single-cell transcriptional profiling of wildtype Rosa26(YFP) (Y) and Kras(G12D) p53(-/-) Rosa26-YFP (KPY) lung AT2 epithelial cells, AT2 organoids, and co-cultured mesenchymal cells with temporal resolution 39 samples shares epithelial, organoids
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.