Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC
Spatial transcriptomics · human · 88 samples
- What it is
- Spatial transcriptomicsGene activity measured with its position in a tissue section.
- Organism
- Homo sapiens (human)
- Topic
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 88 samples: 88 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
- Integrated single-cell and spatial transcriptomics uncover distinct cellular subtypes involved in neural invasion in pancreatic cancerCancer cell · 2025
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 GSE278694_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.
Also filed as BioProject PRJNA1168450. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 35 samples read as cases, 10 as controls.
How we read this: Read from 88 sample titles: 88 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.
- GSM8552940 PA#01, FFPE, high
- GSM8552941 PA#02, FF, high
- GSM8552942 PA#03, FF, high
- GSM8552943 PA#04_1, FFPE, high
- GSM8552944 PA#04_2, FF, high
- GSM8552945 PA#05_1, FFPE, high
- GSM8552946 PA#05_2, CytAssist, high
- GSM8552947 PA#06, FFPE, high
- GSM8552948 PA#08, FF, high
- GSM8552949 PA#11_1, FF, high
- GSM8552950 PA#11_2, CytAssist, high
- GSM8552951 PA#12, CytAssist, low
- GSM8552952 PA#21, CytAssist, high
- GSM8552953 PA#22, CytAssist, low
- GSM8552954 PA#24, CytAssist, low
- GSM8552955 PA#29, CytAssist, high
- GSM8552956 PA#40, CytAssist, high
- GSM8552957 PA#47, CytAssist, low
- GSM8552958 PA#72, CytAssist, low
- GSM8552959 PA#85, CytAssist, high
- GSM8552960 PA#98, CytAssist, high
- GSM8561922 PA#40, Tumor, snRNA
- GSM8561923 PA#21, Tumor, snRNA
- GSM8561924 PA#85, Tumor, snRNA
- GSM8561925 PA#98, Tumor, snRNA
- GSM8561926 PA#72, Tumor, snRNA
- GSM8561927 PA#91, Tumor, snRNA
- GSM8561928 PA#29, Tumor, snRNA
- GSM8561929 PA#24, Tumor, snRNA
- GSM8582554 PA#01, Tumor, scRNA-seq
- GSM8582555 PA#02, Tumor, scRNA-seq
- GSM8582556 PA#04, Tumor, scRNA-seq
- GSM8582557 PA#04, Normal, scRNA-seq
- GSM8582558 PA#05, Tumor, scRNA-seq
- GSM8582559 PA#05, PBMC, scRNA-seq
- GSM8582560 PA#06, Tumor, scRNA-seq
- GSM8582561 PA#06, Normal, scRNA-seq
- GSM8582562 PA#06, PBMC, scRNA-seq
- GSM8582563 PA#07, Tumor, scRNA-seq
- GSM8582564 PA#07, PBMC, scRNA-seq
+ 48 more — browse all 88 samples with per-sample file links →
- GSE101448 Microarray gene-expression data to identify a robust biomarker signature in PDAC and validate it in formalin-fixed paraffin-embedded tissue material. 43 samples same disease briefing · shares pdac
- GSE150043 Deeper insight into Pancreatic Ductal Adenocarcinoma (PDAC) survival heterogeneity using integrative analyses of individual and global transcriptome based networks 19 samples same disease briefing · shares pdac
- GSE71729 Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes. 357 samples same disease briefing · shares subtypes
- GSE102238 Gene expression signatures associated with Perineural Invasion in pancreatic ductal adenocarcinoma 100 samples same disease briefing · shares invasion
- GSE119794 Network-based integration of mRNA and miRNA profiles reveals new target genes involved in pancreatic cancer 40 samples same disease briefing · shares involved
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples same disease briefing · shares single-cell
- GSE268524 A robust circulating microRNA signature for diagnosis and early detection in pancreatobiliary cancer 1403 samples same disease briefing
- GSE143584 Gene expression from laser capture microdissected epithelium and stroma during pancreatic carcinogenesis 366 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.