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Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1

GSE309930 Homo sapiens (human) RNA-seq (gene expression) 10 samples Submitted 2026/04/17 Platform GPL34295
At a glance

RNA-seq (gene expression) · human · 10 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
10 samples: 4 × HEK293T, 1X-Cys, biol vs 4 × HEK293T, 10X-Cys, biol vs 2 × HEK293T, 0X-Cys, biolGroups 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
Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1Nature communications · 2026
Summary (written by the submitters)
Regulation of metabolic enzymes through degradation by the ubiquitin-proteosome system regulation is essential towards maintenance of cellular homeostasis. Our approach directly addresses a problem in the field; linking metabolic signal to an E3 ligase response. We employ active E3 ligase profiling coupled with broad MS-based screening, to reveal the changes in the proteome and E3 ligase-ome in response to the starvation or excess of a specific metabolite.
Read the full summary ↓
We then use computationally driven strategies to connect these responses before in vitro and in cellulo reconstitution. The application of this strategy on cysteine metabolism led to our finding of LRRC58 mediated control of CDO1 degradation. Through reconstitution of this system, we also reveal that endogenous CDO1 degradation by LRRC58 is distinct from degradation induced by a molecular glue. Additionally, we have visualized CDO1 ubiquitylation by an LRRC58 CRL through cryo-EM, demonstrating the structural basis for CDO1 targeting by LRRC58.
Published in
Cysteine availability tunes ubiquitin signaling via inverse stability of LRRC58 E3 ligase and its substrate CDO1
Andree GA, Stier LJ, Schmiederer K et al. · Nature communications 2026 · PMID 42098103 · doi:10.1038/s41467-026-72524-3
This dataset
Open GSE309930 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 GSE309930_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 PRJNA1364011 and SRA study SRP644541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 42098103) ↗
Study design
4 × HEK293T, 1X-Cys, biol vs 4 × HEK293T, 10X-Cys, biol vs 2 × HEK293T, 0X-Cys, biol

Supports a between-group comparison across 10 samples.

How we read this: 3 replicated groups read from 10 sample titles; they account for 10 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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