Smooth Muscle Transcriptome Sequencing Project

University of Nevada, Reno School of Medicine

Mission

Our goal is to elucidate the transcriptome of each population of key cells within smooth muscle (SM) and mucosa (Mu) using deep-sequencing technologies as well as build a SM genome and transcriptome browser which can be used as a reference for all expressed genes.

UCSC Smooth Muscle Genome Browser

UCSC Smooth Muscle Genome Browser

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.

Smooth Muscle Transcriptome Browser

Smooth Muscle Transcriptome Browser

The Smooth Muscle Transcriptome Browser offers expression profiles, isoforms, and cDNAs (ORFs: open reading frames) of each gene expressed in the key cell populations and GI tissues for functional studies.

UCSC Smooth Muscle Methylome Browser

UCSC Smooth Muscle Methylome Browser

The UCSC Smooth Muscle Methylome Browser is an interactive browser which was built with custom tracks representing the methylome and transcriptome of Dnmt1-WT and Dnmt1-KO murine jejunal smooth muscle. This browser provides a comprehensive reference for genomic DNA methylation status at CpG sites in Dnmt1-WT and Dnmt1-KO. The browser can also interact with the genome bioinformatics (e.g. ENCODE) data publically available in the UCSC Genome Browser.

Smooth Muscle Data Repository

Smooth Muscle Data Repository

We have stored transcriptome data files of smooth muscle tissues and cell types, which can be downloaded to build your own custom track UCSC Genome Browser.

Source

Pooled total RNAs were isolated from tissue (2 males and 2 females) or sorted cells (20 males and 20 females) from mice and mRNAs were purified from the total RNAs.

Source materials
NameDescriptionMouse strainBackgroundAgeMolecule
SM_Jejunum Jejunum SM B6.129S7-Kittm1Rosay/J C57BL/6 4 wks mRNA
SMC_Jejunum SMC in jejunum SM B6.Cg-Tg(Myh11-cre,-EGFP)2Mik/J C57BL/6 4 wks mRNA
ICC_Jejunum ICC in jejunum SM B6.129S7-Kittm1Rosay/J C57BL/6 4 wks mRNA
PaC_Jejunum PDGFRα+ cells in jejunum SM B6.129S4-Pdgfratm11(EGFP)Sor/J C57BL/6 4 wks mRNA
SM_Colon Colon SM B6.129S7-Kittm1Rosay/J C57BL/6 4 wks mRNA
SMC_Colon SMC in colon SM B6.Cg-Tg(Myh11-cre,-EGFP)2Mik/J C57BL/6 4 wks mRNA
ICC_Colon ICC in colon SM B6.129S7-Kittm1Rosay/J C57BL/6 4 wks mRNA
PaC_Colon PDGFRα+ cells in colon SM B6.129S4-Pdgfratm11(EGFP)Sor/J C57BL/6 4 wks mRNA
Mu_Colon Colon mucosa B6.129S4-Pdgfratm11(EGFP)Sor/J C57BL/6 4 wks mRNA
PaC_Mu_Colon PDGFRα+ cells in colon mucosa B6.129S4-Pdgfratm11(EGFP)Sor/J C57BL/6 4 wks mRNA

Transcriptome

RNA-seq libraries were generated using Illumina's kit and the libraries were sequenced on Illumina HiSeq 2000 (paired-end sequencing run with 101 nt read length). Sequencing reads were assembled and annotated on the reference genome (UCSC mm9 and/or mm10) using TopHat v1.4.1 software.

Transcriptome by Mapped/Known/Total and Average
NameTotal readMapped readKnown geneTotal isoformAverage isoform
SM_Jejunum 238,246,980 184,746,380 15,837 53,337 3.4
SMC_Jejunum 150,702,388 139,478,151 15,427 46,299 3.0
ICC_Jejunum 206,711,208 177,168,420 17,172 55,259 3.2
PaC_Jejunum 149,419,352 135,517,106 16,270 48,974 3.0
SM_Colon 212,744,016 164,801,684 16,359 55,345 3.4
SMC_Colon 151,445,926 139,645,488 15,192 47,275 3.1
ICC_Colon 193,155,892 168,384,646 16,820 54,488 3.2
PaC_Colon 136,563,090 123,172,778 15,714 48,894 3.1
Mu_Colon 168,835,236 153,208,218 15,933 52,113 3.3
PaC_Mu_Colon 154,151,508 141,592,530 15,777 51,282 3.3

*GI_All: all transcriptional variants expressed in GI cells and tissues above.

CArGome:

A custom Perl script was created to identify CArG elements genome-wide (CArGome) in mice. Conserved CArG boxes were identified via comparison between mouse CArGome and human CArGome.
*CArG_Mouse: Mouse CArG (CC[A/T]6GG) boxes
*CArG_Mouse_and_Human: Conserved CArG boxes in mice and humans

References

UCSC Smooth Muscle Genome Browser

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

Smooth Muscle Transcriptome Browser

Breland A, Ha S, Jorgensen BG, Gardner TA, Sanders KM, Ro S. Smooth Muscle Transcriptome Browser: offering genome-wide references and expression profiles of transcripts expressed in intestinal SMC, ICC, and PDGFRα+ cells (SIP syncytium). In review

UCSC Smooth Muscle Methylome Browser

Jorgensen BG*, Berent RM*, Ha S*, Horiguchi K, Sasse KC, Becker LS, Ro S. DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease. *Equally contributed In review  

Contact

The browsers are developed and maintained by the Reno Smooth Muscle Bioinformatics Team (Director: Dr. Seungil Ro) at the Department of Physiology and Cell Biology in University of Nevada, Reno School of Medicine. If you have feedback or questions concerning the tools or data on this website, feel free to contact us at email: sro@med.unr.edu, phone: (775) 784-1462.