Biomarker-guided responses in patient-derived organoids predict effective therapies in breast cancer
RNA-seq (gene expression) · human · 14 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 14 samples: 14 × patient-derived organoids, sample TORGGroups 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 GSE303509_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 PRJNA1295546 and SRA study SRP603073. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 14 samples.
How we read this: 1 replicated groups read from 14 sample titles; they account for 14 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.
- GSM9128292 patient-derived organoids, sample TORG39 patient-derived organoi…
- GSM9128293 patient-derived organoids, sample TORG40 patient-derived organoi…
- GSM9128294 patient-derived organoids, sample TORG43 patient-derived organoi…
- GSM9128295 patient-derived organoids, sample TORG45 patient-derived organoi…
- GSM9128299 patient-derived organoids, sample TORG51 patient-derived organoi…
- GSM9128300 patient-derived organoids, sample TORG53 patient-derived organoi…
- GSM9128301 patient-derived organoids, sample TORG56 patient-derived organoi…
- GSM9128303 patient-derived organoids, sample TORG58 patient-derived organoi…
- GSM9128304 patient-derived organoids, sample TORG61 patient-derived organoi…
- GSM9128305 patient-derived organoids, sample TORG64 patient-derived organoi…
- GSM9128307 patient-derived organoids, sample TORG139 patient-derived organoi…
- GSM9128308 patient-derived organoids, sample TORG146 patient-derived organoi…
- GSM9785373 patient-derived organoids, sample TORG155 patient-derived organoi…
- GSM9785374 patient-derived organoids, sample TORG565 patient-derived organoi…
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares predict, breast
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE228801 Patient-derived organoids of pancreatic ductal adenocarcinoma for subtype determination and clinical outcome prediction 14 samples shares patient-derived, organoids, predict
- 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, breast
- GSE251958 Predicting patient outcome based on gene-expression biomarkers learned from colorectal cancer organoids and cell lines 21 samples shares organoids, predict
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.