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Early events in transcription and genome organization after STAG2 reconstitution in human cancer cells [RNA-Seq]

GSE318552 Homo sapiens (human) RNA-seq (gene expression) 12 samples Submitted 2026/02/09 Platform GPL24676
At a glance

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 × MOG, adenoviral vector, RNA-Seq, vs 3 × MOG, adeno-STAG2, RNA-Seq, vs 3 × H4, adenoviral vector, RNA-Seq, vs 3 × H4, adeno-STAG2, RNA-Seq,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.
Summary (written by the submitters)
Truncating mutations of the tumor suppressor gene STAG2, encoding a component of the chromatin-bound cohesin complex, are present in many human cancer types. Here we report for the first time the early effects of reconstituting physiological levels of wild-type STAG2 in STAG2-mutant human cancer cells. Acute STAG2 reconstitution only modestly affected global gene expression - <1% of genes were altered by two-fold or greater.
Read the full summary ↓
Only EFEMP1, encoding a secreted extracellular matrix glycoprotein, was induced by STAG2 in all experimental systems tested. There were similarly modest effects on chromatin loops - <1% of all chromatin loops were altered in intensity. and no loops were entirely STAG2-dependent. Loops strengthened by STAG2 reconstitution tended to be small, consistent with prior observations that STAG2-cohesin has less loop extrusion processivity than STAG1-cohesin. The STAG2-regulated “immediate early genes” were not accompanied by STAG2-regulated enhancer-promoter chromatin loops and no chromatin features were identified by integrative bioinformatics with newly generated ChIP-seq and ATAC-seq data that could explain their regulation by STAG2. Together these data indicate that the number of genes directly regulated by STAG2-cohesin is small, suggest that current models are likely insufficient to explain the mechanism of direct transcriptional regulation by STAG2-cohesin, and identify EFEMP1 as a potential effector of STAG2 tumor suppression.
This dataset
Open GSE318552 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 GSE318552_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 PRJNA1419214 and SRA study SRP674923. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × MOG, adenoviral vector, RNA-Seq, vs 3 × MOG, adeno-STAG2, RNA-Seq, vs 3 × H4, adenoviral vector, RNA-Seq, vs 3 × H4, adeno-STAG2, RNA-Seq,

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.

Samples in this study
Datasets on a similar topic

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