A combinatorial ubiquitin code degrades substrates protected by deubiquitylation
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: 3 × Scrambled, vs 3 × siTRIP12, vs 3 × siOTUD5, vs 3 × siTRIP12+siOTUD5,Groups 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
- Combinatorial ubiquitin code degrades deubiquitylation-protected substratesNature communications · 2025
Read the full summary ↓
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE273273_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1141143 and SRA study SRP522682. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 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.
- GSM8425574 Scrambled, rep. 1 Scrambled,
- GSM8425575 Scrambled, rep. 2 Scrambled,
- GSM8425576 Scrambled, rep. 3 Scrambled,
- GSM8425577 siTRIP12, rep. 1 siTRIP12,
- GSM8425578 siTRIP12, rep. 2 siTRIP12,
- GSM8425579 siTRIP12, rep. 3 siTRIP12,
- GSM8425580 siOTUD5, rep. 1 siOTUD5,
- GSM8425581 siOTUD5, rep. 2 siOTUD5,
- GSM8425582 siOTUD5, rep. 3 siOTUD5,
- GSM8425583 siTRIP12+siOTUD5, rep. 1 siTRIP12+siOTUD5,
- GSM8425584 siTRIP12+siOTUD5, rep. 2 siTRIP12+siOTUD5,
- GSM8425585 siTRIP12+siOTUD5, rep. 3 siTRIP12+siOTUD5,
- GSE274723 Combinatorial BMP4 and Activin direct choice between alternate routes to endoderm during human gastrulation. 72 samples shares combinatorial
- GSE301195 Ubiquitin specific peptidase 7 promotes TP53 mutant malignancy by deubiquitinating and stabilizing DDR1 60 samples shares ubiquitin
- GSE318135 β-Lapachone Antagonizes Ubiquitin-Specific Protease 18 Activity to Elicit Anti-Neoplastic Effects 54 samples shares ubiquitin
- GSE274677 Combinatorial BMP4 and Activin direct choice between alternate routes to endoderm during human gastrulation [RNA-seq] 51 samples shares combinatorial
- GSE298471 A combinatorial transcription factor screening platform for immune cell reprogramming [scRNA-seq] 46 samples shares combinatorial
- GSE264375 Combinatorial therapy to target melanoma resistant to immune checkpoint blockade 43 samples shares combinatorial
- GSE328457 Pooled combinatorial screening identifies transcription factor sets that drive hematopoietic progenitor-like cell fate 39 samples shares combinatorial
- GSE324131 A single-cell and spatial atlas of prostate cancer reveals the combinatorial nature of gene modules underlying lineage plasticity and metastasis 38 samples shares combinatorial
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.