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Complex spatial and temporal patterns of gene expression underlie embryodifferentiation, yet methods do not yet exist for the efficient genome-widedetermination of spatial expression patterns during development. In situimaging of transcripts and proteins is the gold-standard, but it is difficultand time consuming to apply to an entire genome, even when highly automated.Sequencing, in contrast, is fast and genome-wide, but is generally applied tohomogenized tissues, thereby discarding spatial information. It is likely thatthese methods will ultimately converge, and we will be able to sequence RNAs insitu, simultaneously determining their identity and location. As a step alongthis path, we developed methods to cryosection individual blastoderm stageDrosophila melanogaster embryos along the anterior-posterior axis and sequencethe mRNA isolated from each 25 micron slice. The spatial patterns of geneexpression we infer closely match patterns previously determined by in situhybridization and microscopy. We applied this method to generate a genome-widetimecourse of spatial gene expression from shortly after fertilization throughgastrulation. We identify numerous genes with spatial patterns that have notyet been described in the several ongoing systematic in situ based projects.This simple experiment demonstrates the potential for combining carefulanatomical dissection with high-throughput sequencing to obtain spatiallyresolved gene expression on a genome-wide scale.

Virtual in situs: Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression