Here we report the transcriptional profiles of 116,312 single cells from mouse embryos collected at nine sequential time points ranging from 6.5 to 8.5 days post-fertilization.
Raw sequencing data are available on ArrayExpress with the following accessions: Atlas: E-MTAB-6967; Smart-seq2 endothelial cells: E-MTAB-6970; Tal1−/− chimaeras: E-MTAB-7325; wild-type chimaeras: E-MTAB-7324. Processed data may be downloaded following the instructions at https://github.com/MarioniLab/EmbryoTimecourse2018. Gene Expression Omnibus (GEO) accession GSE87038 was used to support the annotation of myeloid cells (see Methods). All code is available upon request, and at https://github.com/MarioniLab/EmbryoTimecourse2018. Our atlas can be explored at https://marionilab.cruk.cam.ac.uk/MouseGastrulation2018/. All other data are available from the corresponding authors on reasonable request.