GEO series

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

GSE318550 Homo sapiens (human) Other 8 samples Submitted 2026/02/09 Platform GPL24676

At a glance

human · 8 samples

Organism: Homo sapiens (human)
Samples: 8 samples: 2 × MOG, adenoviral vector, vs 2 × MOG, adeno-STAG2, vs 2 × H4, adenoviral vector, vs 2 × H4, adeno-STAG2,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.

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

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Download · which file do I need?

Direct links to NCBI, 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.

All supplementary files ↗

3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE318550_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

Also filed as BioProject PRJNA1419216. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

2 × MOG, adenoviral vector, vs 2 × MOG, adeno-STAG2, vs 2 × H4, adenoviral vector, vs 2 × H4, adeno-STAG2,

Supports a between-group comparison across 8 samples.

How we read this: 4 replicated groups read from 8 sample titles; they account for 8 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

GSM9497460 MOG, adenoviral vector, rep1 MOG, adenoviral vector,
GSM9497461 MOG, adenoviral vector, rep2 MOG, adenoviral vector,
GSM9497462 MOG, adeno-STAG2, rep1 MOG, adeno-STAG2,
GSM9497463 MOG, adeno-STAG2, rep2 MOG, adeno-STAG2,
GSM9497464 H4, adenoviral vector, rep1 H4, adenoviral vector,
GSM9497465 H4, adenoviral vector, rep2 H4, adenoviral vector,
GSM9497466 H4, adeno-STAG2, rep1 H4, adeno-STAG2,
GSM9497467 H4, adeno-STAG2, rep2 H4, adeno-STAG2,

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