Transcriptional profiling of laser captured intestinal tissue from the planarian Schmidtea mediterranea

Proper function and repair of the digestive system are vital to most animals. Deciphering the mechanisms involved in these processes requires an atlas of gene expression and cell types. Here, we applied laser-capture microdissection (LCM) and RNA-seq to characterize the intestinal transcriptome of Schmidtea mediterranea, a planarian flatworm that can regenerate all organs, including the gut. We identified hundreds of genes with intestinal expression undetected by previous approaches. Systematic analyses revealed extensive conservation of digestive physiology and cell types with other animals, including humans. Furthermore, spatial LCM enabled us to uncover previously unappreciated regionalization of gene expression in the planarian intestine along the medio-lateral axis, especially among intestinal goblet cells. Finally, we identified two intestine-enriched transcription factors that specifically regulate regeneration (hedgehog signaling effector gli-1) or maintenance (RREB2) of goblet cells. Altogether, this work provides resources for further investigation of mechanisms involved in gastrointestinal function, repair and regeneration. Methacarn-fixed planarians were cryosectioned, then medial intestine, lateral intestine, and non-intestinal tissue were collected using laser capture microdissection. Tissue was captured from 10-20 sections from a single animal and pooled for each biological replicate. The experiment was performed in quadruplicate, resulting in 12 samples total (4 medial intestine, 4 lateral intestine, and 4 non-intestine). RNA was extracted using the Arcturus PicoPure RNA Isolation Kit, followed by library generation and RNA-Seq.