ALERT

In Observance of U.S. holiday, Memorial Day, Agilent CrossLab, iLab Operations Software will be closed during U.S. hours and have support during EU and APAC hours on Monday May 29th, 2017. We will resume U.S. support hours on Tuesday May 30th, 2017. For urgent matters, please add "Urgent" to the ticket subject and we will prioritize those requests first.

Thank you,

Proteogenomics Facility

 

Overview of Services

The MUSC Proteogenomics Facility offers a range of genomic services to the MUSC research community as well as to outside academic and corporate researchers. 

 

Instrumentation for independent operation and scheduling:

  • Real time PCR instrumentation (Biorad CFX96)
  • Qubit 2.0 Fluorometer (Life Technologies) for specific and sensitive quantitation of DNA, RNA and protein
  • Monolight 2010 luminometer (BD Biosciences) for luciferase measurement

Genomics:

  • Agilent Bioanalyzer qualitative analysis of RNA and DNA
  • Affymetrix-based transcriptomic profiling (mRNA, microRNA)
  • Affymetrix-based genomic applications (CytoScan® HD Cytogenetic microarray analysis, SNP and ChIP-Chip)
  • Next generation sequencing (Ion Torrent PGM) for selected genomic, amplicon/resequencing and RNA sequencing applications
  • PCR service (large scale projects only) 

Bioinformatics:

  • Microarray-related and DNA sequence-related analyses
  • Training in informatic software
  • Promoter and transcription factor analyses
  • Bioinformatic tool development
  • Web-based storage and distribution of microarray data
  • Data analysis computer workstation equipped with Partek Genomics Suite, Ingenuity Pathway Analysis, dChip, TIGR Multi-experiment Viewer and SPSS software
Currently the facility is supported by:
1) NIH/NIGMS South Carolina COBRE for Cardiovascular Disease (GM103342)
2) NIH/NIGMS South Carolina IDeA Networks of Biomedical Research Excellence (INBRE) (GM103499)
3) Office of the Vice President for Research at the Medical University of South Carolina


Leadership

Director
Jeremy L. Barth, Associate Professor
Medical University of South Carolina
Dept Regenerative Medicine and Cell Biology
Basic Science Building 627, MSC 508
173 Ashley Avenue
Charleston, SC 29425

 

Email: barthj@musc.edu
Phone: (843) 792-9984

 
Email the Facility

 

Location and hours of operation

Hours Location

 9:00 AM to 5:00 PM 

Medical University of South Carolina
Department of Regenerative Medicine and Cell Biology
173 Ashley Avenue, BSB 633
MSC 508
Charleston SC 29425-5080

Links and Resources

  1. Department of Regenerative Medicine & Cell Biology
  2. Barth Laboratory

Publications

  • Scott KK, Norris RA, Potter SS, Norrington DW, Baybo MA, Hicklin DM, Kern MJ. GeneChip microarrays facilitate identification of Protease Nexin-1 as a target gene of the Prx2 (S8) homeoprotein. DNA Cell Biol. 2003 Feb;22(2):95-105. PMID: 12713735
  • Cowart LA, Okamoto Y, Pinto FR, Gandy JL, Almeida JS, Hannun YA. Roles for sphingolipid biosynthesis in mediation of specific programs of the heat stress response determined through gene expression profiling. J Biol Chem. 2003 Aug 8;278(32):30328-38. PMID: 12740364
  • Argraves GL, Barth JL, Argraves WS. The MUSC DNA Microarray Database. Bioinformatics. 2003 Dec 12;19(18):2473-4. PMID: 14668234
  • Rohrer B, Pinto FR, Hulse KE, Lohr HR, Zhang L, Almeida JS. Multidestructive pathways triggered in photoreceptor cell death of the rd mouse as determined through gene expression profiling. J Biol Chem. 2004 Oct 1;279(40):41903-10. PMID: 15218024
  • James ER, Fresco VM, Robertson LL. Glucocorticoid-induced changes in the global gene expression of lens epithelial cells. J Ocul Pharmacol Ther. 2005 Feb;21(1):11-27. PMID: 15718824
  • Pinto FR, Cowart LA, Hannun YA, Rohrer B, Almeida JS. Local correlation of expression profiles with gene annotations - proof of concept for a general conciliatory method. Bioinformatics. 2005 Apr 1;21(7):1037-45. PMID: 15509607
  • Znoiko SL, Rohrer B, Lu K, Lohr HR, Crouch RK, Ma JX. Downregulation of cone-specific gene expression and degeneration of cone photoreceptors in the Rpe65-/- mouse at early ages. Invest Ophthalmol Vis Sci. 2005 Apr;46(4):1473-9. PMID: 15790918
  • Mikhitarian K, Gillanders WE, Almeida JS, Hebert Martin R, Varela JC, Metcalf JS, Cole DJ, Mitas M. An innovative microarray strategy identifies informative molecular markers for the detection of micrometastatic breast cancer. Clin Cancer Res. 2005 May 15;11(10):3697-704. PMID: 15897566
  • Song W, Barth JL, Yu Y, Lu K, Dashti A, Huang Y, Gittinger CK, Argraves WS, Lyons TJ. Effects of Oxidized and Glycated LDL on Gene Expression in Human Retinal Capillary Pericytes. Invest Ophthalmol Vis Sci. 2005 Aug;46(8):2974-82. PMID: 16043874
  • Cowart LA, Okamoto Y, Lu X, Hannun YA. Distinct roles for de novo versus hydrolytic pathways of sphingolipid biosynthesis in Saccharomyces cerevisiae. Biochem J. 2006 Feb 1;393(Pt 3):733-40. PMID: 16201964.
  • Lock EA, Barth JL, Argraves WS, Schnellmann RG. Changes in gene expression in human renal proximal tubule cells exposed to low concentrations of S-1,2-dichlorovinyl-L-cysteine, a metabolite of trichloroethylene. Toxicol Appl Pharmacol. 2006 Oct 15;216(2):319-30. Epub 2006 Jun 8. PMID: 16844155
  • Potter CS, Peterson RL, Barth JL, Pruett ND, Jacobs DF, Kern M, Argraves WS, Sundbergll JP, Awgulewitsch A. The Satin Hair Mutant Gene Foxq1 is among Multiple and Functionally Diverse Regulatory Targets for Hoxc13 during Hair Follicle Differentiation. J Biol Chem. 2006 Sep 29;281(39):29245-55. Epub 2006 Jul 10. PMID: 16835220.
  • Schofield DA Westwater C, Barth JL, DiNovo AA. Development of a biosensor-biocatalyst for the detection and biodegradation of organophosphates. Applied and Environmental Microbiology. Appl Microbiol Biotechnol. 2007 Oct;76(6):1383-94. Epub 2007 Jul 31. PMID: 17665192
  • Barth JL, Yu Y, Song W, Lu K, Dashti A, Huang Y, Argraves WS, Lyons TJ. Oxidised, glycated LDL selectively influences tissue inhibitor of metalloproteinase-3 gene expression and protein production in human retinal capillary pericytes. Diabetologia. 2007 Oct;50(10):2200-8. Epub 2007 Aug 4. PMID: 17676308
  • Wirrig EE, Snarr BS, Chintalapudi MR, O'neal JL, Phelps AL, Barth JL, Fresco VM, Kern CB, Mjaatvedt CH, Toole BP, Hoffman S, Trusk TC, Argraves WS, Wessels A. Cartilage link protein 1 (Crtl1), an extracellular matrix component playing an important role in heart development. Dev Biol. 2007 Oct 15;310(2):291-303. Epub 2007 Aug 9. PMID: 17822691
  • Hammad SM, Twal WO, Barth JL, Smith KJ, Saad AF, Virella G, Argraves WS, Lopes-Virella MF. Oxidized LDL immune complexes and oxidized LDL differentially affect the expression of genes involved with inflammation and survival in human U937 monocytic cells. Atherosclerosis. 2009 Feb;202(2):394-404. Epub 2008 May 28. PMID: 18597759
  • Allen DL, Bandstra ER, Harrison BC, Thorng S, Stodieck LS, Kostenuik PJ, Morony S, Lacey DL, Hammond TG, Leinwand LL, Argraves WS, Bateman TA, Barth JL. Effects of spaceflight on murine skeletal muscle gene expression. J Appl Physiol. 2009 Feb;106(2):582-95. Epub 2008 Dec 12. PMID: 19074574
  • Kitagaki H, Cowart LA, Matmati N, Montefusco D, Gandy J, de Avalos SV, Novgorodov SA, Zheng J, Obeid LM, Hannun YA. ISC1-dependent metabolic adaptation reveals an indispensable role for mitochondria in induction of nuclear genes during the diauxic shift in Saccharomyces cerevisiae. J Biol Chem. 2009 Apr 17;284(16):10818-30. doi: 10.1074/jbc.M805029200. PubMed PMID: 19179331; PubMed Central PMCID: PMC2667769.
  • Jani S, Argraves GL, Barth JL, Argraves WS. GeneMesh: a web-based microarray analysis tool for relating differentially expressed genes to MeSH terms. BMC Bioinformatics. 2010 Apr 1;11:166. PMID: 20359363
  • Barth JL, Clark CD, Fresco VM, Knoll EP, Lee B, Argraves WS, Lee KH. Jarid2 is among a set of genes differentially regulated by Nkx2.5 during outflow tract morphogenesis. Dev Dyn. 2010 Jun 14;239(7):2024-2033. [Epub ahead of print]. PMID: 20549724
  • Baker DA, Barth JL, Chang R, Obeid LM, Gilkeson GS. Genetic sphingosine kinase 1 deficiency significantly decreases synovial inflammation and joint erosions in murine TNFα-induced arthritis. J Immunol. 2010 Aug 15;185(4):2570-9. Epub 2010 Jul 19. PMID: 20644167
  • LaVoie HA, Kordus RJ, Nguyen JB, Barth JL, Hui YY. GATA depletion impacts insulin-like growth factor 1 mRNA and protein levels in luteinizing porcine granulosa cells. Biol Reprod. 2010 Aug 25. [Epub ahead of print]. PMID: 20739664. 
  • Richards AJ, Muller B, Shotwell M, Cowart LA, Rohrer B, Lu X. Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph. Bioinformatics. 2010 Jun 15;26(12):i79-87. doi: 10.1093/bioinformatics/btq203. PubMed PMID: 20529941; PubMed Central PMCID: PMC2881388
  • Gacchina CE, Deb P, Barth JL, Ramamurthi A. Elastogenic inductability of smooth muscle cells from a late-stage rat model of abdominal aortic aneurysms. Tissue Eng Part A. 2011 Jul;17(13-14):1699-711. Epub 2011 May 9. PMID: 21341992
  • Argraves KM, Sethi AA, Gazzolo PJ, Wilkerson BA, Remaley AT, Tybjaerg-Hansen A, Nordestgaard BG, Yeatts SD, Nicholas KS, Barth JL, and Argraves WS. S1P, dihydro-S1P and C24:1-ceramide levels in the HDL-containing fraction of serum inversely correlate with occurrence of ischemic heart disease. Lipids Health Dis. 2011; 10: 70. Published online 2011 May 9. doi: 10.1186/1476-511X-10-70. PMC3116499
  • Embree M, Ono M, Kilts T, Walker D, Mikhail J, Mao J, Bi Y, Barth JL, Young M. Subchondral Bone Defects and Increased Osteoclast Activity in TMJ Osteoarthritis. J Dent Res. 2011 Sep 13. [Epub ahead of print] PMID: 21917603.
  • Jones JA, Stroud RE, O’Quinn EC, Black LE, Barth JL, Elefteriades JA, Bavaria JE, Gorman JH 3rd, Gorman RC, Spinale FG, Ikonomidis JS. Selective microRNA suppression in human thoracic aneurysms: relationship of miR-29a to aortic size and proteolytic induction. Circ Cardiovasc Genet. 2011 Oct 18. [Epub ahead of print] PMID: 22010139.
  • Montefusco DJ, Newcomb B, Gandy JL, Brice SE, Matmati N, Cowart LA, Hannun YA. Sphingoid bases and the serine catabolic enzyme CHA1 define a novel feedforward/feedback mechanism in the response to serine availability. J Biol Chem. 2012 Mar 16;287(12):9280-9. doi: 10.1074/jbc.M111.313445. PubMed PMID: 22277656; PubMed Central PMCID: PMC3308826.
  • Hussey GS, Link LA, Brown AS, Howley BV, Chaudhury A, Howe PH. Establishment of a TGFβ-induced post-transcriptional EMT gene signature. PLoS One. 2012;7(12):e52624. doi: 10.1371/journal.pone.0052624. PubMed PMID: 23285117; PubMed Central PMCID: PMC3527574.
  • KrejcÍ E, Pesevski Z, DeAlmeida AC, Mrug M, Fresco VM, Argraves WS, Barth JL, Cui X, Sedmera D. Microarray analysis of normal and abnormal chick ventricular myocardial development. Physiol Res. 2012;61 Suppl 1:S137-44. PMID: 22827870.
  • Zhang YM, Noto JM, Hammond CE, Barth JL, Argraves WS, Backert S, Peek RM Jr, Smolka AJ. Helicobacter pylori-induced post-transcriptional regulation of H,K-ATPase α subunit gene expression by miRNA. Am J Physiol Gastrointest Liver Physiol. 2014 Feb 6. [Epub ahead of print] PubMed PMID: 24503769.
  • Kang I, Barth JL, Sproul EP, Yoon DW, Braun KR, Argraves WS, Wight TN. Expression of V3 Versican by Rat Arterial Smooth Muscle Cells Promotes Differentiated and Anti-inflammatory Phenotypes. J Biol Chem. 2015 Aug 28;290(35):21629-41. doi: 10.1074/jbc.M115.657486. Epub 2015 Jul 7. PubMed PMID: 26152723; PubMed Central PMCID: PMC4571886.
  • Lang H, Xing Y, Brown LN, Samuvel DJ, Panganiban CH, Havens LT, Balasubramanian S, Wegner M, Krug EL, Barth JL. Neural stem/progenitor cell properties of glial cells in the adult mouse auditory nerve. Sci Rep. 2015 Aug 26;5:13383. doi: 10.1038/srep13383. PubMed PMID: 26307538; PubMed Central PMCID: PMC4549618.
  • Heinrichs J, Li J, Nguyen H, Wu Y, Bastian D, Daethanasanmak A, Sofi MH, Schutt S, Liu C, Jin J, Betts B, Anasetti C, Yu XZ. CD8(+) Tregs promote GVHD prevention and overcome the impaired GVL effect mediated by CD4(+) Tregs in mice. Oncoimmunology. 2016 Mar 28;5(6):e1146842. doi: 10.1080/2162402X.2016.1146842. PubMed PMID: 27471614; PubMed Central PMCID: PMC4938369.
  • Beasley S, Buckhaults PJ, Pedigo NG, Farrell CL. Association of FGD1 polymorphisms with early-onset breast cancer. Oncol Lett. 2016 Sep;12(3):2071-2077. PubMed PMID: 27602141; PubMed Central PMCID: PMC4998584.
  • Lang H, Nishimoto E, Xing Y, Brown LN, Noble KV, Barth JL, LaRue AC, Ando K, Schulte BA. Contributions of Mouse and Human Hematopoietic Cells to Remodeling of the Adult Auditory Nerve After Neuron Loss. Mol Ther. 2016 Oct 4. doi: 10.1038/mt.2016.174. PubMed PMID: 27600399.

Contacts

Name Role Phone Email Location
Jeremy Barth
Director; Primary Technical Contact, Bioinformatics
 
(843) 792-9984
 
barthj@musc.edu
 
BSB 627
 
Cynthia K. Gittinger
Technical Staff; Business Manager
 
(843) 792-6236
 
gittinck@musc.edu
 
BSB 629
 
Reycel Rodriguez
Technical Staff
 
(843) 792-2418
 
rodrigur@musc.edu
 
BSB 633