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| Status |
Public on Jan 26, 2023 |
| Title |
IL-13 signaling via epithelial cell-expressed type II IL-4 receptor mediates eosinophilic esophagitis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: We aimed to define the molecular pathways that are regulated by IL13Ra1 in our experimental murine EoE model
Methods: 1cm piece of the middle part from the esophagus of OXA or Vehicle treated WT or Il13ra1 KO mice were obtained for RNA extraction using TRIZOL. Thereafter, RNA samples were prepared using the CEL-Seq2 protocol, as published by Hashimshony et al. Genome Biology (2016) 17:77, with minor changes. Instead of single-cells as input, 2 ng purified RNA was taken as input for library preparation. 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 EngineeringPurpose: We aimed to define the molecular pathways that are regulated by IL13Ra1 in our experimental murine EoE model.
Results: IL13ra1 regulates transcriptome signature in EoE murine model.
Conclusion: We demonstrate that IL13ra1 results EoE related pathways.
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| Overall design |
RNAseq of esophagus from EoE (OXA) or control (Vehicle) WT or Il13ra1 KO mice
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| Contributor(s) |
Avlas S, Munitz A |
| Citation(s) |
36070083 |
| Submission date |
Jan 25, 2022 |
| Last update date |
Apr 29, 2023 |
| Contact name |
Guy Shapira |
| E-mail(s) |
guyspersonal@gmail.com
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| Organization name |
Tel Aviv University
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| Street address |
Chaim Levanon 30
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| City |
Tel Aviv |
| ZIP/Postal code |
6997801 |
| Country |
Israel |
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| Platforms (1) |
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| Samples (16)
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| Relations |
| BioProject |
PRJNA800267 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE194316_normalized_counts.csv.gz |
1.7 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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