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Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation

GSE288120 Homo sapiens (human) Single-nucleus RNA-seq 35 samples Submitted 2025/09/09 Platform GPL24676
At a glance

Single-nucleus RNA-seq · human · 35 samples

What it is
Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue). Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Topic
Colorectal cancerThis series is part of our curated briefing on it.
Samples
35 samples: 14 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
Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongationNature communications · 2025
Summary (written by the submitters)
Pseudouridine (Ψ) is a widespread RNA modification in various RNA species, including rRNA, tRNA, snRNA and mRNA. Ψ plays a crucial role in RNA metabolism, where it regulates pre-mRNA splicing and affects protein translation. Whether and how Ψ may regulate transcription have not be adequately studied. Here, we report that pseudorudine synthase 7 (PUS7) can mediate pseudouridylation of 7SK small nuclear RNA (snRNA), a regulator of RNA polymerase II (Pol II) promoter-proximal pausing.
Read the full summary ↓
PUS7 loss leads to hypo-pseudouridylation and facilitates sequestration of the positive transcription elongation factor b (P-TEFb) complex from 7SK. The release of P-TEFb from 7SK increases serine 2 phosphorylation (Ser2P) in the RNA Pol II C-terminal domain and enhances transcription elongation. In colorectal cancer (CRC) cells, the Ψ level of 7SK could be modulated by PUS7, or by site-specifically targeted pseudouridylation through dCas13b-guided system. Hypo-pseudouridylation on 7SK with PUS7 depletion promotes KLF6/DDIT3-mediated cell apoptosis and sensitizes CRC cells to 5-FU.
Published in
Pseudouridylation of 7SK by PUS7 regulates Pol II transcription elongation
Zhao Y, Sun HL, Li W et al. · Nature communications 2025 · PMID 41168165 · doi:10.1038/s41467-025-64668-5
This dataset
Open GSE288120 in finder → Find more human RNA-seq datasets → Colorectal cancer landscape →
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 GSE288120_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1216229 and SRA study SRP560146. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41168165) ↗
Study design
14 conditions, mostly in triplicate
HCT116-siCtrl-BID-seq-Input-rp ×3 HCT116-siCtrl-BID-seq-BS-Treated-rp ×3 HCT116-siPUS7-BID-seq-Input-rp ×3 HCT116-siPUS7-BID-seq-BS-Treated-rp ×3 HCT116-siCtrl-mRNA-seq-rp ×3 HCT116-si7SK-mRNA-seq-rp ×3 HCT116-siPUS7-mRNA-seq-rp ×3 HCT116-PUS7-PARclip-rp ×2 +6 more

Supports a case/control comparison: 7 samples read as cases, 8 as controls.

How we read this: 14 replicated groups read from 35 sample titles; they account for 35 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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