To glean an appreciation of the holistic genetic activity in the gastrulating mouse embryo, we performed a genome-wide spatial transcriptome analysis (Stereo-seq), using a low-cell number sequencing protocol on laser microdissected samples of epiblast cells with retained positional address. The 3D transcriptome reveals that (i) the epiblast is partitioned into transcription domains corresponding to regions of epiblast where cells are endowed specifically with ectoderm and mesendoderm potency, (ii) novel lineage markers are identified as genes expressed in epiblast domains populated by cells displaying different lineage fates, (iii) functionally related gene regulatory circuitry and signaling pathways are acting in concert in the transcriptional domains, and (iv) the spatial information provides reference zipcodes for mapping the prospective address of cell samples from different embryos and stem cell lines. The quantified expression data can also be visualized as 3D digitized whole mount in situ hybridization of all the expressed transcripts in the epiblast. SOURCE: Naihe Jing (njing@sibcb.ac.cn) - Stem cell and early development Shanghai Institute of Biochemistry and Cell Biology

Pluto Bioinformatics

GSE65924: Stereo-sequencing: 3D Transcriptome of the mouse embryo at gastrulation