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Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-Wide

GSE261913 Homo sapiens (human) RNA-seq (gene expression) 134 samples Submitted 2025/05/01 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 134 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
134 samples: 129 distinct titles, 3 of them repeatedGroups 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
Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wideACS chemical biology · 2024
Summary (written by the submitters)
Tether-seq uses s4U metabolic labeling to provide sites for reversible and covalent attachment of small molecule disulfides to the transcriptome. By screening under reducing conditions, we are able to highlight interactions that are stabilized by binding over those driven by the reactivity of the RNA sites. When applied to cellular RNA, Tether-seq with a disulfide analogue of risdiplam (compound 2) revealed a number of potential binding sites. Structure probing by SHAPE-MaP revealed a structured motif and confirmed binding to the lead molecule.
Published in
Disulfide Tethering to Map Small Molecule Binding Sites Transcriptome-wide
Moon MH, Vock IW, Streit AD et al. · ACS chemical biology 2024 · PMID 39192734 · doi:10.1021/acschembio.4c00538
This dataset
Open GSE261913 in finder → Find more human 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 GSE261913_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 PRJNA1089575 and SRA study SRP496429. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39192734) ↗
Study design
129 distinct titles, 3 of them repeated
Tether_HEK293T_no_s4U_ctl_Input ×4 Tether_HEK293T_no_s4U_ctl ×2 Tether_HEK293T_s4U_ctl ×2

How we read this: Read from 134 sample titles: 129 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

+ 94 more — browse all 134 samples with per-sample file links →

Datasets on a similar topic

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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.