Bulk RNA sequencing the zebrafish sox17 lineage at 8, 12, and 24 hours post-fertilization

Although much progress has been made in identifying the molecular and genetic factors that contribute to gastrointestinal tract development and disease, how these factors are translated into dynamic cell behaviors that shape the organ is less well understood.  The zebrafish is an excellent model system for studying the cell biology of gut formation in vivo as the embryo develops externally, is optically transparent, and is amenable to numerous methods for manipulating gene function.  The gastrointestinal epithelium is derived from the endoderm.  In zebrafish, endodermal cells are specified just prior to gastrulation and soon after become highly motile and quickly disperse across the inner surface of the embryo.  These scattered cells then undergo a switch in migratory behavior to converge into a coherent endodermal sheet, which ultimately gives rise to the epithelial lining of the gut tube.  The aim of our studies is to identify the cell biological mechanisms driving the transition from single-cell migration to epithelial sheet formation.

Methods
In this study, GFP-positive cells were isolated from transgenic Tg(sox17:GFP)s870 zebrafish embryos by fluorescence activated cell sorting at 8, 12, and 24 hours post-fertlization. Total RNA was extracted from the sorted cells. Library preparation and sequencing was performed by the Genomics Core at the Unviersity of California San Francisco (Core manager, Andrea Barczak; Core director, David Erle).

Sequencing type: Single-end 50bp RNAseq
Library Kit: Illumina TruSeq mRNA stranded
Machine: Illumina HiSeq 4000
Aligner: STAR_2.5.2b
Alignment Genome: Ensembl Zebrafish GRCz10.87