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Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation (RNA-seq).

GSE241565 Homo sapiens (human) RNA-seq (gene expression) 21 samples Submitted 2024/04/29 Platform GPL18573
At a glance

RNA-seq (gene expression) · human · 21 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
21 samples: 7 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
Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activationLife science alliance · 2024
Summary (written by the submitters)
Aims: Evaluate the genome-wide gene expression and epigenomic alterations caused by transient high glucose (HG) in endothelial cells (ECs), and to assess NRF2 pathway activation as a potential treatment for the diabetes-associated transcriptional memory. Methods and results: We exposed human umbilical vein endothelial cells (HUVEC) to three different glucose treatments: control (5.5 mM for 8 days), HG (30 mM for 8 days) and memory (5.5 mM for 4 days followed by 30 mM for 4 days).
Read the full summary ↓
After these treatments we conducted a series of experiments, first we found that cells in the HG treatment had sustained alterations in both glycolytic and respiratory rates that persisted in the memory treatment, this without changes in proliferation or cell viability. Similarly, HG provoked substantial changes in the expression of genes belonging to pathways known to be impaired in diabetes, like the TGF-beta, TNF, foxO, p53 and NRF2 pathways, many of which were still present in memory. In addition, we found persistent changes in chromatin accessibility located mainly in non-promoter regions, some of which we identified as putative enhancer regions neighboring genes altered in memory. Finally, we demonstrated that activation of the NRF2 pathway through either NRF2 overexpression or sulforaphane treatment was able to substantially revert the glucose-induced transcriptional memory in ECs. Conclusions: Our results demonstrate that transient HG induces persistent changes in both the transcriptomic and chromatin accessibility profiles of ECs, and that pharmacological NRF2 pathway activation through sulforaphane supplementation is able to prevent and revert the glucose-induced transcriptional memory.
Published in
Reversal of high-glucose-induced transcriptional and epigenetic memories through NRF2 pathway activation
Wilson-Verdugo M, Bustos-García B, Adame-Guerrero O et al. · Life science alliance 2024 · PMID 38755006 · doi:10.26508/lsa.202302382
This dataset
Open GSE241565 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 GSE241565_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 PRJNA1008711 and SRA study SRP456799. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38755006) ↗
Study design
7 conditions, mostly in triplicate
Control ×3 High_glucose ×3 Memory ×3 HG_NRF2-OE ×3 Memory_NRF2-OE ×3 HG_SF ×3 Memory_SF ×3

Supports a between-group comparison across 21 samples.

How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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
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