GSM4256425: colon, non-infected VAD, replicate 2; Mus musculus; RNA-Seq
Tissue were collected at the end of each study, which were post-infection (p.i.) day 5 for the SI study and p.i. day 10 for the colon study. During tissue collection, the dissected colons were first cut open to remove fecal contents. Both lower SI and colon tissues were snap frozen in liquid nitrogen immediately upon tissue harvest. Total RNA were extracted from frozen intestine samples using the Qiagen RNeasy Midi Kit according to the manufacturer's protocol. Library preparation and sequencing were done in the Penn State Genomics Core Facility (University Park, PA). 200ng of RNA per sample were used as the input of TruSeq Stranded mRNA Library Prep kit to make barcoded libraries according to the manufacturer's protocol (Illumina Inc. San Diego. CA. USA). The library concentration was determined by qPCR using the Library Quantification Kit Illumina Platforms (Kapa Biosystems. Boston. MA. USA). An equimolar pool of the barcoded libraries was made and the pool was sequencing on a HiSeq 2500 system (Illumina) in Rapid Run mode using single ended 150 (SI study) or 100 (colon study) base-pair reads.
GEO Accession
GSM4256425