design: Gut transcriptome analysis in GvHD mice comparing CMKLR1 knockout to wildtype mice
library_construction_protocol: FFPE colon section. Whole transcriptome profiles of gut sections, explanted from allogeneic transplanted mice, were evaluated. Different groups of mice were considered, comparing CMKLR1 knock out vs. Wild type mice. Maxwell 16 LEV RNA FFPE Purification kit (Promega) Whole transcriptome RNA-seq analyses have been performed by Next Generation Sequencing (NGS), using the Universal RNAseq kit (Nugen, Tecan). The Universal RNA-Seq is an end-to-end solution for strand-specific RNA-Seq library construction used 250 ng nanogram amounts of total RNA obtained from gut sections. The workflow consists of double-stranded cDNA generation using a mixture of random priming, optional fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete for globin genes, and PCR amplification to produce the final library. The yields of final libraries were assessed by Qubit 4.0 fluorimeter and their sizing by Agilent Bioanalyzer.