GEO series

Decoding Schwann cell activation in pancreatic cancer neural invasion by mimicking nerve injury responses and using spatial transcriptomics

GSE303707 Homo sapiens (human) Spatial transcriptomics 21 samples Submitted 2026/07/25 Platform GPL24676

At a glance

Spatial transcriptomics · human · 21 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: 21 samples: 7 conditions, mostly in triplicateGroups 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.

Summary (written by the submitters)

Perineural invasion (PNI) is a critical neuropathic change in pancreatic cancer, driven by cancer-nerve interactions, where Schwann cells (SC) undergo reprogramming similar to nerve injury, promoting tumor spread. Despite this, the molecular mechanisms underlying SC activation and their involvement in extrapancreatic PNI remain poorly understood.

Read the full summary ↓

In this study, we drew an analogy between the process of PNI and nerve injury, identifying six nerve injury-related genes (ARRDC4, ATF3, CBFB, NAV2, SNTB1, and TOX) that are highly expressed in SC and implicated in PNI. To certify the role of the selected six genes in neural invasion, the expression of these genes in N008 were knockdown by siRNA.After knocking down the expression of these six genes in N008 cells and performing RNA sequencing, it was found that the knockdown of these genes was associated with the activation of neural pathways, such as axon regeneration, Schwann cell differentiation, axonogenesis, and neurogenesis ,suggesting that these genes likely influence the functions of periphery nervous system.

This dataset

Open GSE303707 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 GSE303707_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: Spatial studies usually ship Space Ranger style folders (count matrix plus tissue images). Look for them among the supplementary files.

Also filed as BioProject PRJNA1297131 and SRA study SRP603791. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

7 conditions, mostly in triplicate

N008 cells,siNC ×3 N008 cells,siARRDC4 ×3 N008 cells,siATF3 ×3 N008 cells,siCBFB ×3 N008 cells,siNAV2 ×3 N008 cells,siSNTB1 ×3 N008 cells,siTOX ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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.

Samples in this study

GSM9134435 N008 cells,siNC 1 N008 cells,siNC
GSM9134436 N008 cells,siNC 2 N008 cells,siNC
GSM9134437 N008 cells,siNC 3 N008 cells,siNC
GSM9134438 N008 cells,siARRDC4 1 N008 cells,siARRDC4
GSM9134439 N008 cells,siARRDC4 2 N008 cells,siARRDC4
GSM9134440 N008 cells,siARRDC4 3 N008 cells,siARRDC4
GSM9134441 N008 cells,siATF3 1 N008 cells,siATF3
GSM9134442 N008 cells,siATF3 2 N008 cells,siATF3
GSM9134443 N008 cells,siATF3 3 N008 cells,siATF3
GSM9134444 N008 cells,siCBFB 1 N008 cells,siCBFB
GSM9134445 N008 cells,siCBFB 2 N008 cells,siCBFB
GSM9134446 N008 cells,siCBFB 3 N008 cells,siCBFB
GSM9134447 N008 cells,siNAV2 1 N008 cells,siNAV2
GSM9134448 N008 cells,siNAV2 2 N008 cells,siNAV2
GSM9134449 N008 cells,siNAV2 3 N008 cells,siNAV2
GSM9134450 N008 cells,siSNTB1 1 N008 cells,siSNTB1
GSM9134451 N008 cells,siSNTB1 2 N008 cells,siSNTB1
GSM9134452 N008 cells,siSNTB1 3 N008 cells,siSNTB1
GSM9134453 N008 cells,siTOX 1 N008 cells,siTOX
GSM9134454 N008 cells,siTOX 2 N008 cells,siTOX
GSM9134455 N008 cells,siTOX 3 N008 cells,siTOX

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