← BioTransfer GEO Dataset Finder
GEO series

A role of DDR2 and substrate stiffness on cancer cell transcriptome and proliferation

GSE246550 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2024/04/19 Platform GPL21697
At a glance

RNA-seq (gene expression) · human · 12 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)
Samples
12 samples: 3 × SH-SY5Y cell line, shCTRL, 24h, 2kPa, vs 3 × SH-SY5Y cell line, shDDR2, 24h, 2kPa, vs 3 × SH-SY5Y cell line, shCTRL, 24h, 20kPa, vs 3 × SH-SY5Y cell line, shDDR2, 24h, 20kPa,Groups 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
DDR2 signaling and mechanosensing orchestrate neuroblastoma cell fate through different transcriptome mechanismsFEBS open bio · 2024
Summary (written by the submitters)
Extracellular matrix (ECM) regulates carcinogenesis. As a major ECM component, collagen interacts with integrin and a non-typical receptor discoidin domain receptor tyrosine kinase 2 (DDR2), but how DDR2 regulates cancer progression is poorly understood. Apart from its signaling function, ECM provides a mechanical environment for cancer, but the impact of biomechanics on cancer remains enigmatic.
Read the full summary ↓
Here, we performed RNA-seq of a human neuroblastoma cell line SH-SY5Y. We found that DDR2 knockdown, but not increasing substrate stiffness, upregulated pro-proliferative genes and down-regulated axonogenesis genes. Surprisingly, despite no transcriptome changes, increasing of stiffness attenuates SH-SY5Y cell proliferation, an effect also observed after DDR2 knockdown. Our results indicate that two ECM effectors, DDR2 and biomechanics, could control cancer cell proliferation through different mechanisms.
Published in
DDR2 signaling and mechanosensing orchestrate neuroblastoma cell fate through different transcriptome mechanisms
Vessella T, Xiang S, Xiao C et al. · FEBS open bio 2024 · PMID 38538106 · doi:10.1002/2211-5463.13798
This dataset
Open GSE246550 in finder → Find more human RNA-seq datasets →
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 GSE246550_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 PRJNA1033608 and SRA study SRP469183. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38538106) ↗
Study design
3 × SH-SY5Y cell line, shCTRL, 24h, 2kPa, vs 3 × SH-SY5Y cell line, shDDR2, 24h, 2kPa, vs 3 × SH-SY5Y cell line, shCTRL, 24h, 20kPa, vs 3 × SH-SY5Y cell line, shDDR2, 24h, 20kPa,

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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
Datasets on a similar topic

Search all human RNA-seq datasets in GEO →

Share this dataset

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.