← BioTransfer GEO Dataset Finder
GEO series

Maternal SMARCA5 is required for major ZGA in mouse [RNA-seq]

GSE248180 Mus musculus (mouse) Single-cell RNA-seq 138 samples Submitted 2024/09/18 Platform GPL19057
At a glance

Single-cell RNA-seq · mouse · 138 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Mus musculus (mouse)
Samples
138 samples: 36 conditions, mostly in duplicateGroups 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)
Zygotic genome activation in mice happens in two waves, a minor wave in the 1 cell embryo, and a major wave at the two-cell stage, both accompanied by global transcriptional and epigenetic reprogramming. However, the orchestration of these reprogramming events by maternal factors deposited in the oocyte is not yet entirely understood.
Read the full summary ↓
We and others have recently shown that epigenetic modifiers such as SMARCA5 (the main ATPase in ISWI complexes), can initiate the ZGA transcriptional programme in vitro. So far, the role of SMARCA5 in ZGA in vivo has not been addressed, as constitutive knock-out mice lacking SMARCA5 are not viable. We have overcome this issue by using the targeted protein-depletion system Trim-Away. Degradation of SMARCA5 in early zygotes in combination with single cell multi-omics methods allow us to investigate its role in transcription, DNA methylation and chromatin accessibility during ZGA, as well as the wider impact of the lack of maternal SMARCA5 on embryonic development. We show that in absence of SMARCA5, major ZGA transcription is downregulated, whereas maternal and other genes are upregulated. Our results show that the global accessibility at the two-cell stage is higher than in a wild-type context, and that major ZGA gene promoters are not following that global trend but remain less accessible in SMARCA5 depleted embryos. Moreover, while the accessibility of repeat elements like MERVL increases, so does the methylation level in these regions, suggesting that SMARCA5 might indirectly influence more than just the chromatin accessibility during these stages.
This dataset
Open GSE248180 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 GSE248180_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1041879 and SRA study SRP472646. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
36 conditions, mostly in duplicate
RNA-seq_SMARCA5 +/+ 2 cell stage embryos (mat… ×3 RNA-seq_SMARCA5 +/+ 2 cell stage embryos (mat… ×3 RNA-seq_SMARCA5 +/- 2 cell stage embryos (ma… ×3 RNA-seq_SMARCA5 +/- 2 cell stage embryos (ma… ×3 RNA-seq_SMARCA5 +/- 2 cell stage embryos (ma… ×3 RNA-seq_SMARCA5 +/- 2 cell stage embryos (ma… ×3 RNA-seq_SMARCA5 +/- 2 cell stage embryos (ma… ×3 RNA-seq_a-Smarca5 TrimAway rep1_A ×3 +85 more

Supports a between-group comparison across 81 samples.

How we read this: 36 replicated groups read from 138 sample titles; they account for 81 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

+ 98 more — browse all 138 samples with per-sample file links →

Datasets on a similar topic

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.