Lysosome Rich Enterocytes mediate protein absorption in the vertebrate gut

The goal of this RNA-seq experiment was to compare gene expression profiles of two different intestinal cell populations (Intestinal epithelial cells that mostly reside in the anterior gut and Lysosome rich enterocytes that reside in mid-intestine) in zebrafish to better understand the characteristics of LREs and uncover the molecular players mediating the function of LREs. Two populations were FACS isolated from 6 days post fertilization (dpf) TgBAC(cldn15la-GFPpd1034) transgenic fish gavaged with Alexa Fluor 568 Dextran 24 hours prior to FACS. RNA was extracted from the FACS sorted cells and expression profiles were determined using Illumina HiSeq. Comparison of the sample groups allowed for identification of unique candidates. The sequence reads that passed quality filters were analyzed using HISAT2, and gene counts were analyzed using HTSeq. Overall design: mRNA profiles of 6 dpf cldn15la-GFP positive intestinal epithelial cells (IECs) and cldn15la-GFP, Alexa Fluor 568 double-positive lysosome rich enterocytes (LREs) were generated by RNA sequencing using Illumina HiSeq 2000. Two distinct samples, with 3 replicates each.