Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methods
RNA-seq (gene expression) · human · 158 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
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 158 samples: 158 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.
- Paper
- Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methodsNPJ precision oncology · 2025
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 GSE313117_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 PRJNA1378562. 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 158 sample titles: 158 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.
- GSM9361352 Pancreatic cancer, patient 2236, whole transcriptome
- GSM9361353 Pancreatic cancer, patient 2447, whole transcriptome
- GSM9361354 Pancreatic cancer, patient 2924, whole transcriptome
- GSM9361355 Pancreatic cancer, patient 2976, whole transcriptome
- GSM9361356 Pancreatic cancer, patient 2977, whole transcriptome
- GSM9361357 Pancreatic cancer, patient 3009, whole transcriptome
- GSM9361358 Pancreatic cancer, patient 3027, whole transcriptome
- GSM9361359 Pancreatic cancer, patient 3030, whole transcriptome
- GSM9361360 Pancreatic cancer, patient 3039, whole transcriptome
- GSM9361361 Pancreatic cancer, patient 3071, whole transcriptome
- GSM9361362 Pancreatic cancer, patient 3109, whole transcriptome
- GSM9361363 Pancreatic cancer, patient 3127, whole transcriptome
- GSM9361364 Pancreatic cancer, patient 3144, whole transcriptome
- GSM9361365 Pancreatic cancer, patient 3165, whole transcriptome
- GSM9361366 Pancreatic cancer, patient 3172, whole transcriptome
- GSM9361367 Pancreatic cancer, patient 3193, whole transcriptome
- GSM9361368 Pancreatic cancer, patient 3196, whole transcriptome
- GSM9361369 Pancreatic cancer, patient 3199, whole transcriptome
- GSM9361370 Pancreatic cancer, patient 3212, whole transcriptome
- GSM9361371 Pancreatic cancer, patient 3220, whole transcriptome
- GSM9361372 Pancreatic cancer, patient 3232, whole transcriptome
- GSM9361373 Pancreatic cancer, patient 3235, whole transcriptome
- GSM9361374 Pancreatic cancer, patient 3250, whole transcriptome
- GSM9361375 Pancreatic cancer, patient 3252, whole transcriptome
- GSM9361376 Pancreatic cancer, patient 3253, whole transcriptome
- GSM9361377 Pancreatic cancer, patient 3275, whole transcriptome
- GSM9361378 Pancreatic cancer, patient 3282, whole transcriptome
- GSM9361379 Pancreatic cancer, patient 3328, whole transcriptome
- GSM9361380 Pancreatic cancer, patient 3337, whole transcriptome
- GSM9361381 Pancreatic cancer, patient 3343, whole transcriptome
- GSM9361382 Pancreatic cancer, patient 3353, whole transcriptome
- GSM9361383 Pancreatic cancer, patient 3554, whole transcriptome
- GSM9361384 Pancreatic cancer, patient 3362, whole transcriptome
- GSM9361385 Pancreatic cancer, patient 3402, whole transcriptome
- GSM9361386 Pancreatic cancer, patient 3408, whole transcriptome
- GSM9361387 Pancreatic cancer, patient 3428, whole transcriptome
- GSM9361388 Pancreatic cancer, patient 3434, whole transcriptome
- GSM9361389 Pancreatic cancer, patient 3444, whole transcriptome
- GSM9361390 Pancreatic cancer, patient 3454, whole transcriptome
- GSM9361391 Pancreatic cancer, patient 3469, whole transcriptome
+ 118 more — browse all 158 samples with per-sample file links →
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 samples same disease briefing · shares capture
- GSE268524 A robust circulating microRNA signature for diagnosis and early detection in pancreatobiliary cancer 1403 samples same disease briefing
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing
- GSE134236 Mutant Kras co-opts a progenitor-derived enhancer network to initiate pancreatic tumorigenesis 166 samples same disease briefing
- GSE81314 Shotgun sequencing of 5-hydroxymethylcysotine circulating cell-free DNA from the blood distinguishes solid tumor tissues of origin 126 samples same disease briefing
- GSE273490 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [CUT&Run] 120 samples same disease briefing
- GSE11838 Pancreatic Tumor vs Various Tissue Normals 107 samples same disease briefing
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.