GSE195658
IL-13 signaling via epithelial cell-expressed type II IL-4 receptor mediates eosinophilic esophagitis  II
Purpose: We aimed to define the molecular pathways and the transcriptome signature of experimental EoE treated WT mice Methods: 1cm piece of the middle part from the esophagus of OXA or Vehicle treated WT mice was obtained for RNA extraction using TRIZOL . Thereafter, RNA samples were prepared for sequencing using the CEL-Seq2 protocol, with minor modifications. Briefly, purified RNA (2 ng) was taken as input for library preparation. Thereafter, the CEL-Seq library was run on an Illumina NextSeq550 instrument. The number of reads ranged from 6,819,051 to 34,217,489 per sample. The reads were mapped to the Mus musculus, GRCm38 genome using Tophat2 version 2.1.0, with up to 2 mismatches allowed per read, the minimum and maximum intron sizes were set to 50 and 100,000, respectively, and an annotation file was provided to the mapper. The percentage of uniquely mapped reads ranged from 86.64% to 90.05% per sample. Only uniquely mapped reads were counted to genes, using 'HTSeq-count' package version 0.6.1 with 'union' mode. Normalization and differential expression analyses were conducted using DESeq2 R package version 1.28.0. Sample preparation, sequencing, quality control, and differential expression analyses were conducted by the "Technion Genome Center," Life Science and Engineering Interdisciplinary Research Center, Technion, Haifa, Israel. Results: Experimental EoE is characterized by predominant inflammation response, proliferation, and epithelial changes. Conclusion:We demonstrate that our new experimental EoE model results with an inflammation signature associated with type 2 immunity Overall design: RNAseq of esophagus  from EoE (OXA) or control (Vehicle) WT mice