Analysis of 3D transcriptomes of mouse gastrulation from Peng et al (2019)

To compare our in vitro differentiation data with the gastrulating mouse embryo, we used the Geo‐Seq data from Peng et al (2019) with accession number {"type":"entrez-geo","attrs":{"text":"GSE120963","term_id":"120963"}}GSE120963. Gene expression levels were log2‐transformed. For each gene, the mean expression level across samples was subtracted to correct for batch effect between mRNA‐Seq and Geo‐Seq. Principal components were computed using only the expression profiles of our in vitro endoderm, mesoderm, and ectoderm differentiation and keeping genes with a 16‐fold variation in expression during endoderm, mesoderm, or ectoderm differentiation and an eightfold variation in expression between different sections of E7.5 embryos. Geo‐Seq expression profiles of E5.5, E6.0, E6.5, E7.0, and E7.5 embryos were projected on the first two principal components.