Patient-derived organoids (PDOs) model treatment response of metastatic gastrointestinal cancers.
RNA-seq (gene expression) · human · 10 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
- 10 samples: 10 samples, each with a distinct title — no replicated groupsGroups 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.
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 GSE108391_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 PRJNA427119 and SRA study SRP127325. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 10 sample titles: 10 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.
- GSM2897301 003 (3770-1032_p.04)
- GSM2897302 004 (3770-1032_p.07)
- GSM2897303 012 (4164-1001_p.06)
- GSM2897304 013 (4164-1001_p.10)
- GSM2897305 016 (4164-1010_p.07)
- GSM2897306 017 (4164-1010_p.09)
- GSM2897307 025 (3994-055_p.05)
- GSM2897308 026 (3994-055_p.10)
- GSM2897309 009 (3994-071_p.05)
- GSM2897310 010 (3994-071_p.12)
- GSE303509 Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer 14 samples shares patient-derived, organoids
- GSE334033 A Patient-Derived Xenograft Model Identifies AK1 as a Key Regulator of Metastatic Potential in Primary Triple-Negative Breast Cancer 105 samples shares patient-derived, metastatic
- GSE210993 RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids 103 samples shares gastrointestinal, organoids
- GSE290695 Identification of Crohn’s disease subtypes in single cell RNA sequencing signatures of treatment naïve samples across the gastrointestinal tract 95 samples shares gastrointestinal, treatment
- GSE210991 5' droplet-based single cell RNA sequencing of human gastrointestinal organoids and Intestinal Metaplasia (IM) organoids [scRNA-seq] 29 samples shares gastrointestinal, organoids
- GSE316195 A Phase 1 clinical trial and single-cell correlates of motixafortide, cemiplimab, gemcitabine and nab-paclitaxel for metastatic treatment-naïve metastatic pancreatic ductal adenocarcinoma. 22 samples shares metastatic, treatment
- GSE291124 snRNA-seq dataset of 17 treatment-naive human PDAC patient-derived tumors 17 samples shares patient-derived, treatment
- GSE339602 Single-cell RNA sequencing of human iPSC-derived forebrain organoids following amyloid-β42 treatment, microglia co-culture, and maraviroc treatment 16 samples shares organoids, treatment
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.