During ontogeny, proliferating cells become restricted in their fate through the combined action of cell-type specific transcription factors and ubiquitous epigenetic machinery, which index chromatin for activity or repression. Although the molecular functions of these regulators are generally well understood, assigning direct developmental roles is hampered by complex mutant phenotypes that often emerge following gastrulation. To investigate these phenotypes comprehensively, we generated a panel of ten essential regulators using a combined zygotic perturbation, single-cell RNA sequencing platform where many mutant embryos can be assayed simultaneously to recover robust transcriptional and morphological information. Deeper analysis of central Polycomb Repressive Complex (PRC) 1 and 2 members indicate substantial cooperativity, but distinguishes a PRC2-dominant role in restricting the germline that emerges from gross molecular changes within the initial conceptus.
This repository contains the collection of R snippets and scripts used to perform the transcriptomics analysis (scRNA-seq) presented in Grosswendt, Kretzmer, Smith et al. The respository is organized in the following subfolders:
- Genotyping repository subfolder
This folder contains all scripts that are used to computationally genotype and thus distinguish single replicates (embryos).
- Scripts repository subfolder
This folder contains all scripts necessary to create the single figure panels from the Source Data files containing the data behind all graphs. Source Data are deposited at https://oc-molgen.gnz.mpg.de/owncloud/s/F8g3y5F79JZRyof.
All scRNA-seq and WGBS datasets can be found in the Gene Expression Omnibus (GEO) under accession code GSE137337.