| URL: | http://med.unr.edu/physio/transcriptome |
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| Description: | The UCSC SM Genome Browser is an interactive browser which was built with custom tracks of transcriptomes from intestinal smooth muscle, mucosa, as well as sorted cells (SMC, ICC, and PDGFRα+ cells) including CArGome [serum response factor (SRF) binding sites] reference sites. This browser provides a comprehensive reference for all transcriptional variants expressed in the cell populations, GI tissues, and genome-wide SRF binding sites. The browser can also interact with the genome bioinformatics (e.g. ENCODE) data publically available in the UCSC Genome Browser |
| Year founded: | 2017 |
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| Accessibility: |
Accessible
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| Country/Region: | United States |
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| University/Institution: | University of Nevada School of Medicine |
| Address: | Department of Physiology and Cell Biology, University of Nevada School of Medicine, Reno, Nevada, United States of America |
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| Country/Region: | United States |
| Contact name (PI/Team): | Seungil Ro |
| Contact email (PI/Helpdesk): | sro@med.unr.edu |
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Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures. [PMID: 28426719]
Transcriptome-scale data can reveal essential clues into understanding the underlying molecular mechanisms behind specific cellular functions and biological processes. Transcriptomics is a continually growing field of research utilized in biomarker discovery. The transcriptomic profile of interstitial cells of Cajal (ICC), which serve as slow-wave electrical pacemakers for gastrointestinal (GI) smooth muscle, has yet to be uncovered. Using copGFP-labeled ICC mice and flow cytometry, we isolated ICC populations from the murine small intestine and colon and obtained their transcriptomes. In analyzing the transcriptome, we identified a unique set of ICC-restricted markers including transcription factors, epigenetic enzymes/regulators, growth factors, receptors, protein kinases/phosphatases, and ion channels/transporters. This analysis provides new and unique insights into the cellular and biological functions of ICC in GI physiology. Additionally, we constructed an interactive ICC genome browser (http://med.unr.edu/physio/transcriptome) based on the UCSC genome database. To our knowledge, this is the first online resource that provides a comprehensive library of all known genetic transcripts expressed in primary ICC. Our genome browser offers a new perspective into the alternative expression of genes in ICC and provides a valuable reference for future functional studies. |