UCSC Smooth Muscle Genome Browser

Department of Physiology and Cell Biology

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.

Access the UCSC Smooth Muscle Genome Browser
(Opens in New Window; Requires Google Chrome and may take a few minutes to upload the large files)

Applications

  1. Searching for isoforms (transcriptional variants) and genomic structure (promoter, exons and introns) for each expressed gene
  2. Searching for genetic regulators (e.g. transcriptional factors)
  3. Searching for epigenetic regulators (e.g. histone modifiers, enhancers, insulators, promoters, locus control regions, and novel elements)
  4. Searching for genetic variation (e.g. SNPs)

Search instructions

  1. To search transcriptional variants of a gene, type in the gene symbol, and click "go."
  2. Under "Custom Tracks," select the view option (e.g., "full") for type of sample (e.g., "SMC_Jejunum"), and click "refresh."
  3. Select the bioinformatics data of interest (e.g., click on "full" under "RefSeq Genes" in "Genes and Gene Predictions" and/or "Caltech TFBS" under "Expression and Regulation" for SRF binding sites), and then click "refresh."
  4. Select options in each bioinformatics data (e.g., click "Caltech TFBS," select "SRF," change the display mode to "full," and click "Submit").
  5. Click "configure" to optimize views (change image width and text size).
  6. To remove any unwanted data, select "hide" in the view option and click "refresh."
  7. Zoom in or out to change views.
  8. To download DNA sequence, go to "View", select "DNA", and click "get DNA" (or "extended case/color options" to modify formatting options).

References

Lee M, Park C, Berent RM, Park PJ, Fuchs R, Syn H, Chin A, Townsend J, Benson CC, Redelman D, Shen T, Park J, Miano JM, Sanders KM, Ro S. Smooth muscle cell genome browser: enabling the identification of novel serum response factor target genesPLoS ONE, 10(8): e0133751, 2015

Lee MY*, Ha SE*, Park C*, Park PJ, Fuchs R, Wei L, Jorgensen BG, Redelman D, Ward SM, Sanders KM, Ro S. Transcriptome of interstitial cells of Cajal reveals unique and selective gene signaturesPLoS One, 12(4):e0176031, 2017 *Equally contributed

Ha S, Lee MY, Kurahashi M, Wei L, Jorgensen BG, Park C, Park PJ, Redelman D, Sasse KC, Becker LS, Sanders KM, Ro S. Transcriptome analysis of PDGFRα+ cells identifies T-type Ca2+ channel CACNA1G as a new pathological marker for PDGFRα+ cell hyperplasiaPLoS One, 12(8):e0182265, 2017

Ha S, Lee MY, Kurahashi M, Jorgensen BG, Wei L, Park C, Park PJ, Sasse KC, Becker LS, Sanders KM, Ro S. Transcriptome profiling of colonic subepithelial PDGFRα+ cells unveils a metalloendopeptidase ADAM-Like Decysin 1 as a selective marker for Crohn's diseaseIn submission