GEO series

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation [RNA-seq]

GSE246954 Mus musculus (mouse) RNA-seq (gene expression) 24 samples Submitted 2024/03/21 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 24 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: Mus musculus (mouse)
Samples: 24 samples: 6 conditions, mostly with about 4 replicates eachGroups 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: Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenationeLife · 2024

Summary (written by the submitters)

Partial reprogramming by cyclic short-term expression of Yamanaka factors holds promise for shifting cells to younger states and consequently delaying the onset of many diseases of aging. However, the delivery of transgenes and potential risk of teratoma formation present challenges forin vivoapplications. Recent advances include the use of cocktails of compounds to reprogram somatic cells, but the characteristics and mechanisms of partial cellular reprogramming by chemicals remain unclear.

Read the full summary ↓

Here, we report a multi-omics characterization of partial chemical reprogramming in fibroblasts from young and aged mice. We measured the effects of partial chemical reprogramming on the epigenome, transcriptome, proteome, phosphoproteome, and metabolome. At the transcriptome, proteome, and phosphoproteome levels, we saw widescale changes induced by this treatment, with the most notable signature being an upregulation of mitochondrial oxidative phosphorylation. Furthermore, at the metabolome level, we observed a reduction in the accumulation of aging-related metabolites. Using both transcriptomic and epigenetic clock-based analyses, we show that partial chemical reprogramming reduces the biological age of mouse fibroblasts. We demonstrate that these changes have functional impacts, as evidenced by changes in cellular respiration and mitochondrial membrane potential. Taken together, these results illuminate the potential for chemical reprogramming reagents to rejuvenate aged biological systems, and warrant further investigation into adapting these approaches forin vivoage reversal.

Published in

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation

Mitchell W, Goeminne LJE, Tyshkovskiy A et al. · eLife 2024 · PMID 38517750 · doi:10.7554/eLife.90579

This dataset

Open GSE246954 in finder → Find more mouse 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 GSE246954_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 PRJNA1035317 and SRA study SRP470047. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38517750) ↗

Study design

6 conditions, mostly with about 4 replicates each

20mo, untreated, ×4 20mo, 7c treated, ×4 20mo, 2c treated, ×4 4mo, untreated, ×4 4mo, 7c treated, ×4 4mo, 2c treated, ×4

Supports a between-group comparison across 24 samples.

How we read this: 6 replicated groups read from 24 sample titles; they account for 24 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

GSM7881367 20mo, untreated, replicate 1 20mo, untreated,
GSM7881368 20mo, 7c treated, replicate 1 20mo, 7c treated,
GSM7881369 20mo, 2c treated, replicate 1 20mo, 2c treated,
GSM7881370 20mo, untreated, replicate 2 20mo, untreated,
GSM7881371 20mo, 7c treated, replicate 2 20mo, 7c treated,
GSM7881372 20mo, 2c treated, replicate 2 20mo, 2c treated,
GSM7881373 20mo, untreated, replicate 3 20mo, untreated,
GSM7881374 20mo, 7c treated, replicate 3 20mo, 7c treated,
GSM7881375 20mo, 2c treated, replicate 3 20mo, 2c treated,
GSM7881376 20mo, untreated, replicate 4 20mo, untreated,
GSM7881377 20mo, 7c treated, replicate 4 20mo, 7c treated,
GSM7881378 20mo, 2c treated, replicate 4 20mo, 2c treated,
GSM7881379 4mo, untreated, replicate 1 4mo, untreated,
GSM7881380 4mo, 7c treated, replicate 1 4mo, 7c treated,
GSM7881381 4mo, 2c treated, replicate 1 4mo, 2c treated,
GSM7881382 4mo, untreated, replicate 2 4mo, untreated,
GSM7881383 4mo, 7c treated, replicate 2 4mo, 7c treated,
GSM7881384 4mo, 2c treated, replicate 2 4mo, 2c treated,
GSM7881385 4mo, untreated, replicate 3 4mo, untreated,
GSM7881386 4mo, 7c treated, replicate 3 4mo, 7c treated,
GSM7881387 4mo, 2c treated, replicate 3 4mo, 2c treated,
GSM7881388 4mo, untreated, replicate 4 4mo, untreated,
GSM7881389 4mo, 7c treated, replicate 4 4mo, 7c treated,
GSM7881390 4mo, 2c treated, replicate 4 4mo, 2c treated,

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