GEO series
Changes in gene expression patterns in young and senescent fibroblasts in glycated three-dimensional collagen matrices
GSE293225
Homo sapiens (human)
RNA-seq (gene expression)
36 samples
Submitted 2025/06/04
Platform GPL11154
At a glance
RNA-seq (gene expression) · human · 36 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
- 36 samples: 36 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
- Changes in Gene Expression Patterns in Young and Senescent Fibroblasts in Glycated Three-Dimensional Collagen MatricesInternational journal of molecular sciences · 2025
Summary (written by the submitters)
Glycation, or non-enzymatic glycosylation, has recently attracted increasing interest in the context of its impact on aging. Advanced glycation end products (AGEs) contribute to various age-related pathological conditions such as inflammation, fibrosis, stem cell aging, etc. However, the molecular mechanisms underlying the glycation-induced disruption of cell-matrix interactions during cellular senescence are not fully understood.
Read the full summary ↓
The aim of this study was to investigate transcriptomic changes in young and senescent dermal fibroblasts (HdFbs) cultivated in post-glycated 3D collagen type I matrices after 10 and 17 days. Our findings indicate that the D-ribose-mediated glycation increases the accumulation of fluorescent AGEs and the stiffness of the matrices in a dose-dependent manner. The transcriptome alterations encompassed the modulation of age-related genes and signaling pathways, including the activation of genes related to senescence-associated secretory phenotype (SASP) in young cells. Notably, the alterations in the transcriptome profiles due to glycation were more pronounced (in terms of both the number of genes and their fold changes) on day 10 of cultivation compared to day 17 in both passages.
Published in
Guvatova ZG, Kudasheva ER, Efremov YM et al.
· International journal of molecular sciences 2025
· PMID 40429909
· doi:10.3390/ijms26104769
This dataset
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.
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 GSE293225_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1243382 and SRA study SRP573888. Searching any of these in the dataset finder brings you back here.
Study design
36 samples, each with a distinct title — no replicated groups
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 36 sample titles: 36 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.
Samples in this study
- GSM8878899 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 1replicate
- GSM8878900 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 2replicate
- GSM8878901 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 3replicate
- GSM8878902 HdFbs at 20th passage, 5mg/mL collagen, 15mm D-ribose, 10days, 1replicate
- GSM8878903 HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 2replicate
- GSM8878904 HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 3replicate
- GSM8878905 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 1replicate
- GSM8878906 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 2replicate
- GSM8878907 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 3replicate
- GSM8878908 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 1replicate
- GSM8878909 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 2replicate
- GSM8878910 HdFbs at 20th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 3replicate
- GSM8878911 HdFbs at 20th passage, 5mg/mL collagen, 15mm D-ribose, 17days, 1replicate
- GSM8878912 HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 2replicate
- GSM8878913 HdFbs at 20th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 3replicate
- GSM8878914 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 1replicate
- GSM8878915 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 2replicate
- GSM8878916 HdFbs at 20th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 3replicate
- GSM8878917 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 1replicate
- GSM8878918 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 2replicate
- GSM8878919 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 10days, 3replicate
- GSM8878920 HdFbs at 12th passage, 5mg/mL collagen, 15mm D-ribose, 10days, 1replicate
- GSM8878921 HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 2replicate
- GSM8878922 HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 10days, 3replicate
- GSM8878923 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 1replicate
- GSM8878924 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 2replicate
- GSM8878925 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 10days, 3replicate
- GSM8878926 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 1replicate
- GSM8878927 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 2replicate
- GSM8878928 HdFbs at 12th passage, 5mg/mL collagen, 0mM D-ribose, 17days, 3replicate
- GSM8878929 HdFbs at 12th passage, 5mg/mL collagen, 15mm D-ribose, 17days, 1replicate
- GSM8878930 HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 2replicate
- GSM8878931 HdFbs at 12th passage, 5mg/mL collagen, 15mM D-ribose, 17days, 3replicate
- GSM8878932 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 1replicate
- GSM8878933 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 2replicate
- GSM8878934 HdFbs at 12th passage, 5mg/mL collagen, 30mM D-ribose, 17days, 3replicate
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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.