Computational protocol: Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo

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Protocol publication

[…] Intestinal epithelial cells were isolated from the colons of 8–12 week old mice at 0, 4, and 11 days post-DSS treatment. For each timepoint, 2 Tfeb ΔIEC and 2 Tfeb flox/flox animals were used as biological replicates. RNA was extracted by tissuelyzer treatment followed by RNeasy (Qiagen). Full length cDNA libraries were prepared using template switching and whole transcriptome amplification in a slight variation of the SmartSeq. 2 protocol described in. Libraries were sequenced on a MiSeq machine (Illumina). Paired-end reads were mapped to the mm10 reference genome using Tophat2+ Bowtie. Differential gene expression was determined using Cuffdiff. A corrected p-value (q-value) of 0.05 was considered significant. Mapped reads were deposited in GEO with accession number GSE98266. Clustering analysis of differentially expressed genes was performed using Pearson correlation implemented in Morpheus (software.broadinstitute.org/morpheus). GO enrichment analysis was performed for each gene cluster using g:profiler. […]

Pipeline specifications

Software tools Bowtie, Cufflinks, g:Profiler
Databases Full Length cDNA
Application RNA-seq analysis
Organisms Caenorhabditis elegans, Homo sapiens, Mus musculus
Diseases Colitis, Crohn Disease, Wounds and Injuries