GEO series

Podocytes from Hypertensive and Obese Mice Acquire an Inflammatory, Senescent and Aged Phenotype

GSE255723 Mus musculus (mouse) RNA-seq (gene expression) 34 samples Submitted 2024/07/03 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 34 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: 34 samples: 34 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: Podocytes from hypertensive and obese mice acquire an inflammatory, senescent, and aged phenotypeAmerican journal of physiology. Renal physiology · 2024

Summary (written by the submitters)

Patients with hypertension or obesity can develop glomerular dysfunction characterized by injury and depletion of podocytes. To better understand the molecular processes involved, young mice were treated with either deoxycorticosterone acetate (DOCA) or fed a high-fat diet (HFD) to induce hypertension or obesity, respectively. The transcriptional changes associated with these phenotypes were measured by unbiased bulk mRNA-sequencing of isolated podocytes from experimental models and their respective controls.

Read the full summary ↓

Key findings were validated by immunostaining. In addition to a decrease in canonical proteins and reduced podocyte number, podocytes from both hypertensive and obese mice exhibited a sterile inflammatory phenotype characterized by increases in NLRP3 inflammasome, protein cell death-1, and Toll-Like Receptor pathways. Finally, although the mice were young, podocytes in both models exhibited increased expression of senescence and aging genes, including genes consistent with a senescence-associated secretory phenotype. However, there were differences between the hypertension- and obesity-associated senescence phenotypes. Both show stress-induced podocyte senescence characterized by increased p21 and p53. Moreover, in hypertensive mice, this is superimposed upon age-associated podocyte senescence characterized by increased p16 and p19. These results suggest that senescence, aging, and inflammation are critical aspects of the podocyte phenotype in experimental hypertension and obesity in mice.

Published in

Podocytes from hypertensive and obese mice acquire an inflammatory, senescent, and aged phenotype

McKinzie SR, Kaverina N, Schweickart RA et al. · American journal of physiology. Renal physiology 2024 · PMID 38420674 · doi:10.1152/ajprenal.00417.2023

This dataset

Open GSE255723 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 GSE255723_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 PRJNA1076227 and SRA study SRP489751. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38420674) ↗

Study design

34 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 34 sample titles: 34 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

GSM8078433 26461-P, 5.5 months, rep1
GSM8078434 26462-P, 5.5 months, rep2
GSM8078435 26463-P, 5.5 months, rep3
GSM8078436 26464-P, 5.5 months, rep4
GSM8078437 26465-P, 5.5 months, rep5
GSM8078438 26466-P, 5.5 months, rep6
GSM8078439 26467-P, 5.5 months, rep7
GSM8078440 26468-P, 5.5 months, rep8
GSM8078441 26469-P, 5.5 months, rep9
GSM8078442 26470-P, 5.5 months, rep10
GSM8078443 26005-P, 5.5 months with DOCA, rep1
GSM8078444 26006-P, 5.5 months with DOCA, rep2
GSM8078445 26007-P, 5.5 months with DOCA, rep3
GSM8078446 26008-P, 5.5 months with DOCA, rep4
GSM8078447 26009-P, 5.5 months with DOCA, rep5
GSM8078448 26103-P, 5.5 months with DOCA, rep6
GSM8078449 26104-P, 5.5 months with DOCA, rep7
GSM8078450 26105-P, 5.5 months with DOCA, rep8
GSM8078451 26106-P, 5.5 months with DOCA, rep9
GSM8078452 26451-P, 7 months, rep1
GSM8078453 26452-P, 7 months, rep2
GSM8078454 26453-P, 7 months, rep3
GSM8078455 26454-P, 7 months, rep4
GSM8078456 26455-P, 7 months, rep5
GSM8078457 26456-P, 7 months, rep6
GSM8078458 26457-P, 7 months, rep7
GSM8078459 26458-P, 7 months, rep8
GSM8078460 26459-P, 7 months, rep9
GSM8078461 26460-P, 7 months, rep10
GSM8078462 26106-P_HFD, 7 months with HFD, rep1
GSM8078463 26107-P, 7 months with HFD, rep2
GSM8078464 26132-P, 7 months with HFD, rep3
GSM8078465 26134-P, 7 months with HFD, rep4
GSM8078466 26135-P, 7 months with HFD, rep5

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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.