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Recruitment to the nuclear periphery enhances repression of H3K9me2-marked genes and transposons to shape cell fate [RNAseq_shLBR]

GSE264602 Mus musculus (mouse) RNA-seq (gene expression) 43 samples Submitted 2024/08/09 Platform GPL24247
At a glance

RNA-seq (gene expression) · mouse · 43 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
43 samples: 11 conditions, mostly with about 4 replicates eachGroups 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
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fatebioRxiv : the preprint server for biology · 2024
Summary (written by the submitters)
Heterochromatic loci marked by histone H3 lysine 9 dimethylation (H3K9me2) are enriched at the nuclear periphery in metazoans, but the functional importance of this organization is unknown. Both the nuclear lamins and the nuclear membrane protein lamin B receptor (LBR) have been linked to heterochromatin positioning in mammals, yet embryonic stem cells (mESCs) lacking all lamins retain both LBR and H3K9me2 at the nuclear periphery.
Read the full summary ↓
We ablated LBR in this context and show that heterochromatin detaches from the nuclear periphery in lamin + LBR quadruple knockout (QKO) cells. QKO mESCs sustain naïve pluripotency and maintain H3K9me2 at normal levels across the genome but cannot repress H3K9me2-marked genes or transposons. Further, their capacity to differentiate into epiblast-like cells (EpiLCs) is impaired. While normal EpiLCs expand H3K9me2 across the genome, QKO EpiLCs exhibit abnormal patterning of this mark. QKO cells can exit naïve pluripotency and activate epiblast-stage genes but also express markers of alternative fates including the primitive endoderm. These results establish that recruitment of H3K9me2 to the nuclear periphery controls the spatial position, dynamic remodeling, and repressive capacity of this mark to shape cell fate decisions.
Published in
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate
Marin H, Simental E, Allen C et al. · bioRxiv : the preprint server for biology 2024 · PMID 39026839 · doi:10.1101/2024.07.08.602542
This dataset
Open GSE264602 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 GSE264602_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 PRJNA1103227 and SRA study SRP503431. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39026839) ↗
Study design
11 conditions, mostly with about 4 replicates each
mESC, naive pluripotency, TKO, shLUC, day0, ×4 mESC, naive pluripotency, TKO, shLUC, day1, ×4 mESC, naive pluripotency, TKO, shLUC, day4, ×4 mESC, naive pluripotency, TKO, shLBR, day0, ×4 mESC, naive pluripotency, TKO, shLBR, day1, ×4 mESC, naive pluripotency, TKO, shLBR, day2, ×4 mESC, naive pluripotency, TKO, shLBR, day4, ×4 mESC, naive pluripotency, WT, ×4 +3 more

Supports a between-group comparison across 43 samples.

How we read this: 11 replicated groups read from 43 sample titles; they account for 43 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

+ 3 more — browse all 43 samples with per-sample file links →

Datasets on a similar topic

Search all mouse 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.