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Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis

GSE143584 Homo sapiens (human) RNA-seq (gene expression) 366 samples Submitted 2026/03/02 Platform GPL11154Platform GPL20301
At a glance

RNA-seq (gene expression) · human · 366 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
366 samples
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.
Summary (written by the submitters)
This study used laser capture microdissection to obtain highly purified epithelial and stromal RNA samples from frozen sections of human pancreatic ductal adenocarcinoma (PDA), low-grade pancreatic intraepithelial neoplasias (PanIN) and low-grade intraductal papillary mucinous neoplasms (IPMN). Libraries were prepared using the Nugen Ovation RNA-Seq System V2 and sequenced to a depth of 30 million 100bp single-end reads.
Read the full summary ↓
These data were used to reconstruct both an epithelial and stromal gene regulatory network of malignant pancreatic disease using the ARACNE algorithm and elucidate regulatory proteins whose dysregulation drives progression and dedifferentiation in PDA.
This dataset
Open GSE143584 in finder → Find more human RNA-seq datasets → Pancreatic cancer landscape →
Download · which file do I need?

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.

1 · Just have a look

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.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE143584_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
3 · Start from the raw reads

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.

Raw reads on ENA ↗

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 PRJNA600982 and SRA study SRP241805. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
A cohort of 366 individual samples

The grouping that defines any comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Sample titles run S1 … S395 and carry no group information.

Samples in this study

+ 326 more — browse all 366 samples with per-sample file links →

More Pancreatic cancer datasets

Search all human RNA-seq datasets in GEO →

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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.