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RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited

GSE222656 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 40 samples Submitted 2026/08/08 Platform GPL28457Platform GPL30172
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 40 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
40 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.
Summary (written by the submitters)
We have found that lamin B1 is dissociated from the nuclear envelope transiently at the 2-cell stage during mouse embryonic development. This lamin B1 dissociation is mediated by autophagy and can be inhibited by interfering with lamin B1’s binding to LC3, a factor responsible for early autophagosome formation. In order to block interaction between lamin B1 and LC3, we injected mRNA harboring the LC3-binding domain of lamin B1 to mouse embryos and examined transcriptomes of the injected embryos by RNA sequencing (RNA-seq) analysis.
Read the full summary ↓
In addition, embryos expressed with full-length lamin B1 mRNA harboring two different types of mutations (flLB1(F454A/L457A) and flLB1(5A)) were analyzed by RNA-seq, together with non-injection control (Non2). Another injection control (flLB1(F454A/L457A)ΔC) was also performed, together with a non-injection control (Non3). Furthermore, the effect of nuclear stiffening was examined by expressing the molecular tether-anchor system (tWT), together with a mutant carrying LaG165A (tMut) and a non-injection control (Non4). Chromatin states of such embryos were analyzed by Cut & Tag using anti-H3K4me3 antibody.
This dataset
Open GSE222656 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 GSE222656_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA922971 and SRA study SRP417039. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
12 conditions, mostly in triplicate
LC3 ×4 Non ×4 flLB1(F454A/L457A) ×3 flLB1(5A) ×3 Non2 ×3 tWT ×3 tMut ×3 Non4 ×3 +8 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 40 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
Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

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