Evaluation of epithelial growth from colon organoids in Transwell systems and the impact of growth factors
RNA-seq (gene expression) · human · 21 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
- Homo sapiens (human)
- Samples
- 21 samples: 20 distinct titles, 1 of them repeatedGroups 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
- Human colon organoid Transwell model for investigating epithelial growth and repairnpj biomedical innovations · 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 GSE319169_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 PRJNA1422242 and SRA study SRP676293. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 21 sample titles: 20 distinct titles with little repetition. 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.
- GSM9512848 GMD1.A
- GSM9512849 GMD1.B
- GSM9512850 GMD2.A
- GSM9512851 GMD2.B
- GSM9512852 DiffD1.A
- GSM9512853 DiffD1.B
- GSM9512854 DiffD3.A
- GSM9512855 DiffD3.B
- GSM9512856 DiffD5.A
- GSM9512857 DiffD5.B
- GSM9512858 DiffD7.A
- GSM9512859 DiffD7.B
- GSM9512860 Organoid A
- GSM9512861 Organoid B
- GSM9512862 Ctrl
- GSM9512863 EGF
- GSM9512864 TGFa
- GSM9512865 KGF
- GSM9512866 TFF3
- GSM9512867 IL2
- GSM9512868 IL10
- GSE288617 Paired transcriptomics reveals similarities between cytokine-stimulated organoids and ulcerative colitis epithelial responses 41 samples shares epithelial, organoids
- GSE289912 APOE4 impacts cortical neurodevelopment and alters network formation in human brain organoids 32 samples shares organoids, impact
- GSE288517 Paired transcriptomics reveals similarities between cytokine-stimulated organoids and ulcerative colitis epithelial responses 23 samples shares epithelial, organoids
- GSE301790 RNA Sequencing Analysis of PFAS Impact on Liver Organoids 9 samples shares organoids, impact
- GSE318601 Early differential impact of MeCP2 mutations on functional networks in Rett syndrome patient-derived human cortical organoids [RNA-Seq] 8 samples shares organoids, impact
- GSE292059 Inflammatory Epithelial and Macrophage Pathways Underlie Residual Asthma Exacerbations in Urban Children Treated with Mepolizumab 965 samples shares epithelial
- GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 samples shares epithelial
- GSE302560 Effect of calcium oxalate microcrystals on kidney proximal tubule epithelial cell gene expression in microgravity 144 samples shares epithelial
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.