Transcriptional profiling of pancreatic somatostatin and beta-cells from zebrafish [scRNA-seq]

Pancreas contains a collection of different types of endocrine cells. Each endocrine cell secretes a specific hormone. Using reporter lines for two hormones, insulin and somatostatin1.1, we observe the presence of bi-hormonal cells in zebrafish pancreas. To characterize the cells at transcriptional level, we performed next-generation RNA-Sequencing on FACS sorted cells expressing sst1.1, ins, or both sst1.1 and ins. Overall design: We used fluorescence-activated cell sorting (FACS) coupled with next generation RNA-Sequencing to profile sst1.1+ somatostatin, ins+ beta- and sst1.1+ ins+ cells from 30 dpf animals. Cells were sorted directly into lysis buffer and cDNA prepared using Smart-Seq2. Sequencing was performed on llumina NextSeq500. Reads were splice-aligned to the zebrafish genome, GRCz11, using HISAT2. Featurecounts was used to assign reads to exons thus eventually getting counts per gene.