GEO series

Regulation of Mammalian Cellular Metabolism by Endogenous Cyanide Production [TST_RNA-Seq]

GSE286106 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2025/01/09 Platform GPL24676

At a glance

RNA-seq (gene expression) · human · 12 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: 12 samples: 4 × WT_CT vs 4 × shTST_CT vs 4 × overTST_CTGroups 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: Regulation of mammalian cellular metabolism by endogenous cyanide productionNature metabolism · 2025

Summary (written by the submitters)

Small, gaseous molecules – such as nitric oxide (NO), carbon monoxide (CO) and hydrogen sulfide (H2S) are produced as signalling molecules in mammalian cells. Here, we show that low concentrations of cyanide are generated endogenously in various mammalian tissues and cells. We detect cyanide in several cellular compartments of human cells and in various tissues and the blood of mice.

Read the full summary ↓

Cyanide production is stimulated by glycine, occurs at the low pH of lysosomes and requires peroxidase activity. When generated at a specific rate, cyanide exerts stimulatory effects on mitochondrial bioenergetics, cell metabolism, and cell proliferation, but impairs cellular bioenergetics at high concentrations. Cyanide can modify cysteine residues via protein S-cyanylation, which is detectable basally in cells and mice, and increases in response to glycine. Low-dose cyanide supplementation exhibits cytoprotective effects in hypoxia and reoxygenation models in vitro and in vivo. Conversely, pathologically elevated cyanide production in nonketotic hyperglycinemia is detrimental to cells. Our findings indicate that cyanide should be considered part of the same group of endogenous mammalian regulatory gasotransmitters as NO, CO and H2S.

Published in

Regulation of mammalian cellular metabolism by endogenous cyanide production

Zuhra K, Petrosino M, Janickova L et al. · Nature metabolism 2025 · PMID 40033006 · doi:10.1038/s42255-025-01225-w

This dataset

Open GSE286106 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 GSE286106_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 PRJNA1207942 and SRA study SRP556016. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40033006) ↗

Study design

4 × WT_CT vs 4 × shTST_CT vs 4 × overTST_CT

Supports a between-group comparison across 12 samples.

How we read this: 3 replicated groups read from 12 sample titles; they account for 12 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

GSM8717820 WT_CTR1 WT_CT
GSM8717821 WT_CTR2 WT_CT
GSM8717822 WT_CTR3 WT_CT
GSM8717823 WT_CTR4 WT_CT
GSM8717824 shTST_CTR1 shTST_CT
GSM8717825 shTST_CTR2 shTST_CT
GSM8717826 shTST_CTR3 shTST_CT
GSM8717827 shTST_CTR4 shTST_CT
GSM8717828 overTST_CTR1 overTST_CT
GSM8717829 overTST_CTR2 overTST_CT
GSM8717830 overTST_CTR3 overTST_CT
GSM8717831 overTST_CTR4 overTST_CT

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Search all human RNA-seq datasets in GEO →

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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.