Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type Mice and Toll-like Receptor 4 Intestianl Epithelial Conditional Knockout Mice Ileal Transcriptomes

Toll-like receptor 4 (TLR4), the receptor of gram-negative bacterial endotoxin, is present on the intestinal epithelium and plays pivotal roles in intestinal epithelial differentiation and host defense. To better understand TLR4 on the intestinal epithelium, the ileum samples from wild type mice and mice lacking TLR4 in the intestinal epithelium (TLR4?IEC) were subjected to RNA-seq analysis to interrogate the transcriptome. We mapped about 20 million sequence reads per sample to the mouse genome and identified 86477 genes in the ileum of wild type and TLR4?IEC mice. 455 genes were differentially expressed between wild type and TLR4?IEC mice and 1037 genes were absent either from wild type or TLR4?IEC mice with G-factor value 0.015 and ? cutoff value 0.54. Pathway analysis via IPA indicated some impacted canonical KEGG pathways such as DNA replication, PPAR signaling, Toll-like receptor signaling, cytokine-cytokine interaction, adherens junction, Jak-STAT signaling, and tight junction. Overall design: Total RNA was isolated from the ileum of 3 wild type mice and 3 TLR4?IEC mice, and a barcode was added to the sample from each individual mouse during the whole transcriptome library preparation. The pooled samples from 3 wild type mice (barcodes BC01, BC02 and BC03) and from 3 TLR4?IEC mice (barcodes BC07, BC08 and BC09) were subjected to RNA sequencing, respectively.