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Maintenance of gene expression homeostasis by systems-level feedback loops in response to changes in RNA polymerase II dosage [RNAPII_levels_mRNAseq]

GSE307861 Homo sapiens (human) RNA-seq (gene expression) 42 samples Submitted 2025/11/19 Platform GPL34281
At a glance

RNA-seq (gene expression) · human · 42 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
42 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.
Summary (written by the submitters)
Transcription is regulated by sequence-specific transcription factors and enzymes allowing access to genes in chromatin. However, recent data indicate that the abundance of RNA polymerase II (RNAPII) may itself under certain circumstances represent an additional, crucial determinant of transcription regulation. Here, we titrated the cellular dosage of human RPB1, the largest RNAPII subunit, using the dTAG system to more generally assess the importance of RNAPII levels.
Read the full summary ↓
Unexpectedly, cells are extremely sensitive to RPB1 dosage, with a mere 30% reduction sufficient to perturb cell proliferation, cell cycle progression, and global transcription. Using a combination of sequencing and proteomic approaches, we uncover the existence of multiple feedback loops between transcriptional initiation, promotor-proximal pause release, transcript elongation, splicing, and mRNA half-life, which facilitate the maintenance of gene expression homeostasis. Together, our data suggests that gene expression is highly sensitive to RPB1 dosage and that the cellular levels of RNAPII must be tightly regulated.
This dataset
Open GSE307861 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 GSE307861_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 PRJNA1327427 and SRA study SRP619292. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
14 conditions, mostly in triplicate
RPB1degron_DMSO ×3 RPB1degron_2nM_dTAGv1 ×3 RPB1degron_4nM_dTAGv1 ×3 RPB1degron_8nM_dTAGv1 ×3 RPB1degron_16nM_dTAGv1 ×3 RPB1degron_32nM_dTAGv1 ×3 RPB1degron_62nM_dTAGv1 ×3 RPB1degron_83nM_dTAGv1 ×3 +6 more

Supports a between-group comparison across 42 samples.

How we read this: 14 replicated groups read from 42 sample titles; they account for 42 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

+ 2 more — browse all 42 samples with per-sample file links →

Datasets on a similar topic

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.