Perturbing nuclear glycosylation in the mouse preimplantation embryo slows down embryonic growth

This website shows the results of the analyses of RNA-Seq data for paper "Perturbing nuclear glycosylation in the mouse preimplantation embryo slows down embryonic growth" (Formichetti et al. 2024).

Source Rmd code is in github repository.

2-cell embryos

• Analysis of publicly available Smart-Seq data of pre-EGA and post-EGA 2-cell embryos
• Filtering steps and clustering of 2-cell embryos injected with Btgh/dBtgh or non-injected
• Analysis of differential gene expression in 2-cell embryos injected with Btgh/dBtgh or non-injected
• Gene set enrichment analysis in 2-cell embryos injected with Btgh
• Analysis of retrotransposons expression in 2-cell embryos injected with Btgh/dBtgh or non-injected

Morulae

• Filtering steps and clustering of morulae injected with Btgh/dBtgh or non-injected
• Analysis of differential gene expression in morulae injected with Btgh/dBtgh or non-injected
• Gene set enrichment analysis in morulae injected with Btgh
• Analysis of retrotransposons expression in morulae injected with Btgh/dBtgh or non-injected

Blastocysts

• Filtering steps and clustering of blastocysts injected with Btgh/dBtgh or non-injected
• Analysis of differential gene expression in blastocysts injected with Btgh/dBtgh or non-injected
• Gene set enrichment analysis in blastocysts injected with Btgh
• Comparison of GSEA results for morulae and blastocysts injected with Btgh
• Dynamics of differentially expressed genes (DEGs) at the three preimplantation stages upon Btgh injection
• PCA of the single embryos from the three preimplantation stages non-injected or injected with Btgh/dBtgh
• Testing parental chromosomal imbalance with allele-specific analysis of RNA-Seq counts from FVB/PWD F1 blastocysts
• Analysis of retrotransposons expression in blastocysts injected with Btgh/dBtgh or non-injected

E7 embryos

Note: in all reports, EPI and TROPHO denote the embryonic and extraembryonic halves in which the E7 embryos were cut, largely corresponding to the epiblast (deriving from the blastocyst ICM) and extraembryonic ectoderm (deriving from the blastocyst trophectoderm) tissues.

• Filtering steps and clustering of E7 embryos injected with Btgh or dBtgh
• Analysis of differential gene expression in E7 embryos injected with Btgh or dBtgh
• Gene set enrichment analysis in E7 embryos injected with Btgh
• Assessment of developmental delay of single E7 epiblasts from Btgh-inj. embryos based on mesoderm markers and DNAme enzymes
• Counts of Btgh/dBtgh mRNA molecules, Ogt and Oga transcripts at all analyzed embryonic stages after Btgh injection

Publicly available mRNA-Seq data spanning mouse early development (GSE66582 and GSE76505, only wild-type embryos)

• Ogt and Oga transcript isoforms across early development
• Analysis of differential gene expression between consecutive mouse preimplantation stages
• Dynamics across preimplantation stages of genes coherently deregulated upon nuclear O-GlcNAc removal in 2-cell embryos, morulae and blastocysts, as well as of all ribosomal protein genes
• Dynamics across early development of DNAme enzymes as well as DEGs found in single E7 epiblasts from Btgh-inj. embryos
• Dynamics across preimplantation stages of genes associated with PC1/2 of PCA of 2-cell embryos, morulae and blastocysts from our study
• Analysis of retrotransposons expression across preimplantation stages