GEO series

Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organization

GSE287837 Mus musculus (mouse) RNA-seq (gene expression) 36 samples Submitted 2025/06/05 Platform GPL21493

At a glance

RNA-seq (gene expression) · mouse · 36 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: Mus musculus (mouse)
Samples: 36 samples: 12 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: Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organisationNature communications · 2025

Summary (written by the submitters)

Mouse heterochromatin is characterised by transcriptionally competent major satellite repeat (MSR) sequences and it has been proposed that MSR RNA contributes to the integrity of heterochromatin. We established an inducible dCas9-effector system in mouse embryonic fibroblasts, where we can modulate MSR transcription through the targeting of a dCas9-Repressor or a dCas9-Activator.

Read the full summary ↓

With this system, we can define a threshold limit of >300-fold deregulation of MSR transcript levels, above which the structural organisation of heterochromatin becomes disrupted. MEF cells expressing MSR RNA above this threshold limit are not viable and the defects in heterochromatin organisation and chromosome segregation cannot be reverted. This study highlights the importance of restricting MSR RNA output to maintain heterochromatin integrity and relates MSR transcript levels to either physiological or pathological conditions. It also reveals that the structural organisation of heterochromatin is governed by the transcriptional chromatin state and associated MSR RNA of the MSR repeats.

Published in

Forced expression of MSR repeat transcripts above a threshold limit breaks heterochromatin organisation

Ching RW, Świst-Rosowska KM, Erikson G et al. · Nature communications 2025 · PMID 40645983 · doi:10.1038/s41467-025-61586-4

This dataset

Open GSE287837 in finder → Find more mouse 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 GSE287837_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 PRJNA1214800 and SRA study SRP559541. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40645983) ↗

Study design

12 conditions, mostly in triplicate

MSR-dCas9-Control MEF, timecourse, uninduced, ×3 MSR-dCas9-Control MEF, timecourse, induced, ×3 MSR-dCas9-Control MEF, timecourse, post-induc… ×3 MSR-dCas9-Control MEF, timecourse, post-induc… ×3 MSR-dCas9-Control MEF, timecourse, post-induc… ×3 MSR-dCas9-Control MEF, timecourse, post-induc… ×3 MSR-dCas9-Activator MEF, timecourse, uninduce… ×3 MSR-dCas9-Activator MEF, timecourse, induced, ×3 +4 more

Supports a case/control comparison: 6 samples read as cases, 12 as controls.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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

GSM8752206 MSR-dCas9-Control MEF, timecourse, uninduced, rep1 MSR-dCas9-Control MEF, …
GSM8752207 MSR-dCas9-Control MEF, timecourse, uninduced, rep2 MSR-dCas9-Control MEF, …
GSM8752208 MSR-dCas9-Control MEF, timecourse, uninduced, rep3 MSR-dCas9-Control MEF, …
GSM8752209 MSR-dCas9-Control MEF, timecourse, induced, rep1 MSR-dCas9-Control MEF, …
GSM8752210 MSR-dCas9-Control MEF, timecourse, induced, rep2 MSR-dCas9-Control MEF, …
GSM8752212 MSR-dCas9-Control MEF, timecourse, induced, rep3 MSR-dCas9-Control MEF, …
GSM8752213 MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep1 MSR-dCas9-Control MEF, …
GSM8752214 MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep2 MSR-dCas9-Control MEF, …
GSM8752215 MSR-dCas9-Control MEF, timecourse, post-induction 3h, rep3 MSR-dCas9-Control MEF, …
GSM8752216 MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep1 MSR-dCas9-Control MEF, …
GSM8752218 MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep2 MSR-dCas9-Control MEF, …
GSM8752219 MSR-dCas9-Control MEF, timecourse, post-induction 6h, rep3 MSR-dCas9-Control MEF, …
GSM8752220 MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep1 MSR-dCas9-Control MEF, …
GSM8752221 MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep2 MSR-dCas9-Control MEF, …
GSM8752222 MSR-dCas9-Control MEF, timecourse, post-induction 12h, rep3 MSR-dCas9-Control MEF, …
GSM8752223 MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep1 MSR-dCas9-Control MEF, …
GSM8752225 MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep2 MSR-dCas9-Control MEF, …
GSM8752226 MSR-dCas9-Control MEF, timecourse, post-induction 24h, rep3 MSR-dCas9-Control MEF, …
GSM8752227 MSR-dCas9-Activator MEF, timecourse, uninduced, rep1 MSR-dCas9-Activator MEF…
GSM8752228 MSR-dCas9-Activator MEF, timecourse, uninduced, rep2 MSR-dCas9-Activator MEF…
GSM8752229 MSR-dCas9-Activator MEF, timecourse, uninduced, rep3 MSR-dCas9-Activator MEF…
GSM8752230 MSR-dCas9-Activator MEF, timecourse, induced, rep1 MSR-dCas9-Activator MEF…
GSM8752232 MSR-dCas9-Activator MEF, timecourse, induced, rep2 MSR-dCas9-Activator MEF…
GSM8752233 MSR-dCas9-Activator MEF, timecourse, induced, rep3 MSR-dCas9-Activator MEF…
GSM8752234 MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep1 MSR-dCas9-Activator MEF…
GSM8752235 MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep2 MSR-dCas9-Activator MEF…
GSM8752236 MSR-dCas9-Activator MEF, timecourse, post-induction 3h, rep3 MSR-dCas9-Activator MEF…
GSM8752237 MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep1 MSR-dCas9-Activator MEF…
GSM8752239 MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep2 MSR-dCas9-Activator MEF…
GSM8752240 MSR-dCas9-Activator MEF, timecourse, post-induction 6h, rep3 MSR-dCas9-Activator MEF…
GSM8752241 MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep1 MSR-dCas9-Activator MEF…
GSM8752242 MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep2 MSR-dCas9-Activator MEF…
GSM8752243 MSR-dCas9-Activator MEF, timecourse, post-induction 12h, rep3 MSR-dCas9-Activator MEF…
GSM8752244 MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep1 MSR-dCas9-Activator MEF…
GSM8752246 MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep2 MSR-dCas9-Activator MEF…
GSM8752247 MSR-dCas9-Activator MEF, timecourse, post-induction 24h, rep3 MSR-dCas9-Activator MEF…

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