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Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR

GSE255574 Homo sapiens (human) RNA-seq (gene expression) 45 samples Submitted 2024/08/21 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 45 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
45 samples: 15 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.
Paper
Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTORProceedings of the National Academy of Sciences of the United States of America · 2024
Summary (written by the submitters)
Previous studies have demonstrated that the physical properties of biomaterials can be adjusted to program therapeutically relevant functions in encapsulated mesenchymal stromal cells (MSCs). However, the intracellular pathways affected by mechanical cues in this cell type are not well understood. An understanding of the pertinent factors involved would not only aid in the rational design of substrates but also uncover targetable mechanisms that can facilitate the engineering of MSCs for cell therapies.
Read the full summary ↓
Here, a bone marrow-mimetic hydrogel is employed to systematically explore the stiffness-responsive transcriptome of MSCs. High matrix rigidity impedes integrin-collagen adhesions which yields changes in cell morphology that are characterized by a contractile network of actin proximal to the cell membrane. This results in a suppression of ECM-regulatory genes involved in the remodeling of collagen fibrils and an upregulation of secreted immunomodulatory factors. Moreover, an investigation of long non-coding RNAs reveals that CYTOR contributes to these stiffness-driven changes in gene abundance. A robust knockdown of CYTOR using antisense oligonucleotides enhances the expression of numerous mechanoresponsive cytokines and chemokines to levels exceeding what is achievable by modulating matrix stiffness alone. Taken together, these findings emphasize the utility in studying previously unexplored mechanisms of mechanotransduction to inform novel strategies for enhancing the efficacy of MSC-based therapies.
Published in
Matrix stiffness-dependent regulation of immunomodulatory genes in human MSCs is associated with the lncRNA CYTOR
Lim JJ, Vining KH, Mooney DJ et al. · Proceedings of the National Academy of Sciences of the United States of America 2024 · PMID 39074278 · doi:10.1073/pnas.2404146121
This dataset
Open GSE255574 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 GSE255574_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 PRJNA1075642 and SRA study SRP489345. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39074278) ↗
Study design
15 conditions, mostly in triplicate
poly(A),MSC,150Pa,24hr,dmso,n ×3 poly(A),MSC,150Pa,24hr,blebb,n ×3 poly(A),MSC,150Pa,48hr,dmso,n ×3 poly(A),MSC,150Pa,48hr,blebb,n ×3 poly(A),MSC,500Pa,24hr,dmso,n ×3 poly(A),MSC,500Pa,24hr,blebb,n ×3 poly(A),MSC,500Pa,48hr,dmso,n ×3 poly(A),MSC,500Pa,48hr,blebb,n ×3 +7 more

Supports a between-group comparison across 45 samples.

How we read this: 15 replicated groups read from 45 sample titles; they account for 45 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

+ 5 more — browse all 45 samples with per-sample file links →

Datasets on a similar topic

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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.