GEO series

Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [RNA-Seq 2]

GSE276046 Homo sapiens (human) Single-cell RNA-seq 28 samples Submitted 2024/09/24 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 28 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism: Homo sapiens (human)
Samples: 28 samples: 14 conditions, mostly in duplicateGroups 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)

Finite replicative potential is a defining feature of non-transformed somatic cells, first established by Leonard Hayflick in vitro using WI-38 human lung fibroblasts. Once proliferative capacity is exhausted due to telomere shortening, cells enter into a state called replicative senescence, which can be avoided through ectopic expression of telomerase reverse transcriptase (hTERT).

Read the full summary ↓

As WI-38 cells approach replicative arrest, molecular pathways linked to mechanotransduction are induced, including YAP signaling, but the potential interplay between replicative lifespan and the mechanical environment of the cell remains unexplored. Here, we investigate the influence of mechanosensation on the trajectory towards replicative arrest taken by WI-38 cells by growing cells on substrates of varying stiffnesses. Matrix softening slowed proliferation, altered cellular phenotypes, and shortened proliferative lifespan while hTERT expression abrogated or reduced these responses. Our analyses of bulk and single-cell RNA-sequencing and ATAC-sequencing revealed the emergence of a unique G1 transcriptional state on soft substrates, characterized by an AP-1 transcription factor program, which failed to manifest with hTERT expression. Together, these findings reveal how the mechanical environment alters WI-38 cell proliferative lifespan and dictates unique paths towards growth arrest.

This dataset

Open GSE276046 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 GSE276046_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1154571 and SRA study SRP529738. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

14 conditions, mostly in duplicate

WT, 2.3GPa, timepoint 1, RNA-Seq 2, ×2 WT, 2kPa, timepoint 1, RNA-Seq 2, ×2 WT, 6.6MPa, timepoint 1, RNA-Seq 2, ×2 WT, 0.7MPa, timepoint 1, RNA-Seq 2, ×2 WT, 0.4MPa, timepoint 1, RNA-Seq 2, ×2 WT, 2.3GPa, timepoint 2, RNA-Seq 2, ×2 WT, 2kPa, timepoint 2, RNA-Seq 2, ×2 WT, 6.6MPa, timepoint 2, RNA-Seq 2, ×2 +6 more

Supports a between-group comparison across 28 samples.

How we read this: 14 replicated groups read from 28 sample titles; they account for 28 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

GSM8490175 WT, 2.3GPa, timepoint 1, RNA-Seq 2, replicate 1 WT, 2.3GPa, timepoint 1…
GSM8490176 WT, 2.3GPa, timepoint 1, RNA-Seq 2, replicate 2 WT, 2.3GPa, timepoint 1…
GSM8490177 WT, 2kPa, timepoint 1, RNA-Seq 2, replicate 1 WT, 2kPa, timepoint 1, …
GSM8490178 WT, 2kPa, timepoint 1, RNA-Seq 2, replicate 2 WT, 2kPa, timepoint 1, …
GSM8490179 WT, 6.6MPa, timepoint 1, RNA-Seq 2, replicate 1 WT, 6.6MPa, timepoint 1…
GSM8490180 WT, 6.6MPa, timepoint 1, RNA-Seq 2, replicate 2 WT, 6.6MPa, timepoint 1…
GSM8490181 WT, 0.7MPa, timepoint 1, RNA-Seq 2, replicate 1 WT, 0.7MPa, timepoint 1…
GSM8490182 WT, 0.7MPa, timepoint 1, RNA-Seq 2, replicate 2 WT, 0.7MPa, timepoint 1…
GSM8490183 WT, 0.4MPa, timepoint 1, RNA-Seq 2, replicate 1 WT, 0.4MPa, timepoint 1…
GSM8490184 WT, 0.4MPa, timepoint 1, RNA-Seq 2, replicate 2 WT, 0.4MPa, timepoint 1…
GSM8490185 WT, 2.3GPa, timepoint 2, RNA-Seq 2, replicate 1 WT, 2.3GPa, timepoint 2…
GSM8490186 WT, 2.3GPa, timepoint 2, RNA-Seq 2, replicate 2 WT, 2.3GPa, timepoint 2…
GSM8490187 WT, 2kPa, timepoint 2, RNA-Seq 2, replicate 1 WT, 2kPa, timepoint 2, …
GSM8490188 WT, 2kPa, timepoint 2, RNA-Seq 2, replicate 2 WT, 2kPa, timepoint 2, …
GSM8490189 WT, 6.6MPa, timepoint 2, RNA-Seq 2, replicate 1 WT, 6.6MPa, timepoint 2…
GSM8490190 WT, 6.6MPa, timepoint 2, RNA-Seq 2, replicate 2 WT, 6.6MPa, timepoint 2…
GSM8490191 WT, 0.7MPa, timepoint 2, RNA-Seq 2, replicate 1 WT, 0.7MPa, timepoint 2…
GSM8490192 WT, 0.7MPa, timepoint 2, RNA-Seq 2, replicate 2 WT, 0.7MPa, timepoint 2…
GSM8490193 WT, 0.4MPa, timepoint 2, RNA-Seq 2, replicate 1 WT, 0.4MPa, timepoint 2…
GSM8490194 WT, 0.4MPa, timepoint 2, RNA-Seq 2, replicate 2 WT, 0.4MPa, timepoint 2…
GSM8490195 WT, 2.3GPa, timepoint 3, RNA-Seq 2, replicate 1 WT, 2.3GPa, timepoint 3…
GSM8490196 WT, 2.3GPa, timepoint 3, RNA-Seq 2, replicate 2 WT, 2.3GPa, timepoint 3…
GSM8490197 WT, 6.6MPa, timepoint 3, RNA-Seq 2, replicate 1 WT, 6.6MPa, timepoint 3…
GSM8490198 WT, 6.6MPa, timepoint 3, RNA-Seq 2, replicate 2 WT, 6.6MPa, timepoint 3…
GSM8490199 WT, 0.7MPa, timepoint 3, RNA-Seq 2, replicate 1 WT, 0.7MPa, timepoint 3…
GSM8490200 WT, 0.7MPa, timepoint 3, RNA-Seq 2, replicate 2 WT, 0.7MPa, timepoint 3…
GSM8490201 WT, 0.4MPa, timepoint 3, RNA-Seq 2, replicate 1 WT, 0.4MPa, timepoint 3…
GSM8490202 WT, 0.4MPa, timepoint 3, RNA-Seq 2, replicate 2 WT, 0.4MPa, timepoint 3…

Datasets on a similar topic

GSE276045 Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [RNA-Seq 1] 178 samples shares wi-38, proliferative, substrate, stiffness, dictates, towards, rna-seq, unique
GSE276047 Substrate stiffness dictates unique paths towards proliferative arrest in WI-38 cells [ATAC-Seq] 36 samples shares wi-38, proliferative, substrate, stiffness, dictates, towards, unique
GSE282384 Substrate Stiffness Dictates Unique Doxorubicin-induced Senescence-associated Secretory Phenotypes and Transcriptomic Signatures in Human Pulmonary Fibroblasts 12 samples shares substrate, stiffness, dictates, unique
GSE246550 A role of DDR2 and substrate stiffness on cancer cell transcriptome and proliferation 12 samples shares substrate, stiffness
GSE288557 ULK1 as a novel therapeutic target in Myeloproliferative Neoplasms [RNA-Seq] 12 samples shares proliferative, rna-seq
GSE229742 RNA-seq of CAF05s grown on different substrates 12 samples shares substrate, rna-seq
GSE327733 Galectin-1 Fuels Monocyte-Driven Hyperinflammation and Represents a Novel Therapeutic Target in Myeloproliferative Neoplasms [RNA-Seq] 10 samples shares proliferative, rna-seq
GSE329316 Transcriptome sequencing of cavernous fibroblasts cultured on substrates with different stiffness. 9 samples shares substrate, stiffness

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