Computational protocol: Desmoglein-1 regulates esophageal epithelial barrier function and immune responses in eosinophilic esophagitis

Similar protocols

Protocol publication

[…] RNA isolated from esophageal biopsies of 6 NL and 10 patients with active EoE (mean eosinophils/HPF = 164 ± 29 SEM) was subjected to RNA sequencing at the CCHMC Gene Discovery and Genetic Variation Core as previously described. The paired-end sequencing reads were aligned against the GRCh37 genome model using TopHat 2.04 with Bowtie 2.03, . The separate alignments were then merged using Cuffmerge with RefSeq gene models as a reference. The aligned reads were then quantified for differential expression analysis using Cuffdiff. Statistical significance was determined using a t-test with a threshold of p < 5 × 10−2 and a 2.0-fold cut-off filter in GeneSpringR 11.5 (Agilent Technologies Incorporated, Clara, CA, USA). […]

Pipeline specifications

Software tools TopHat, Bowtie, Cufflinks
Application RNA-seq analysis
Organisms Homo sapiens
Diseases Drug Hypersensitivity, Genetic Diseases, Inborn, Eosinophilic Esophagitis