Computational protocol: R-Spondins Are Expressed by the Intestinal Stroma and are Differentially Regulated during Citrobacter rodentium- and DSS-Induced Colitis in Mice

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Protocol publication

[…] Total RNA of whole colon tissues from uninfected and infected C3Ou and C3Ou.B6-Cri1 mice was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions. A cleanup of the samples was done using the RNeasy Plus Micro Kit (Qiagen). The RNA integrity number, assessed by a Bioanalyzer (Agilent), was 8.0 and above for all RNA samples. Sequencing was performed at the McGill University and Genome Quebec Innovation Center using Illumina HiSeq 2000/2500 technology with three libraries per lane to generate 110–187 million paired reads per library. The data was aligned to the mm10 mouse genome assembly (http://genome.ucsc.edu/cgi-bin/hgGateway?db=mm10) with the combination of the TopHat/Bowtie software []. The Cufflinks program [] was used to calculate the relative abundance of select transcripts of interest, expressed in FPKM (“fragments per kilobase of exon per million fragments mapped”) units. Human gene expression data were acquired from the Human Protein Atlas (http://www.proteinatlas.org/), available through the ArrayExpress Archive (http://www.ebi.ac.uk/arrayexpress/) under the accession number E-MTAB-2836. […]

Pipeline specifications

Software tools TopHat, Bowtie, Cufflinks
Databases ArrayExpress Human Protein Atlas
Application RNA-seq analysis
Organisms Mus musculus, Citrobacter rodentium, Homo sapiens
Diseases Colitis, Crohn Disease, Infection, Inflammatory Bowel Diseases