ALERT

In Observance of the Christmas Holidays, Agilent Cross Lab/ iLab Operations Software will be closed during U.S. hours on Monday December 24th and Tuesday December 25th, 2018. We will resume regular U.S. support hours on Wednesday December 26th, 2018. For urgent matters, please add "Urgent" to the ticket/ email subject or press "1", when prompted, to escalate a call on the iLab Support phone and we will prioritize those requests first.

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)
  • NanoDrop One for spectrophotometric analysis
  • 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)
  • Next generation sequencing (Ion Torrent PGM) for selected genomic, amplicon/resequencing and RNA sequencing applications
  • PCR service (large scale projects only) 

PCR:

  • RT-qPCR: reverse transcription and quantitative PCR analysis service
  • Genotyping: PCR amplification with user-provided primers/template and agarose gel analysis

Bioinformatics:

  • Microarray-related and DNA sequence-related analyses
  • Training in informatic software
  • Promoter and transcription factor analyses
  • Data analysis computer workstation equipped with dChip, MeV
Currently the facility is supported by:
1) NIH/NIGMS South Carolina IDeA Networks of Biomedical Research Excellence (INBRE) (GM103499)
2) 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

Recent Publications

  • 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.
  • Beiko T, Janech MG, Alekseyenko AV, Atkinson C, Coxson HO, Barth JL, Stephenson SE, Wilson CL, Schnapp LM, Barker A, Brantly M, Sandhaus RA, Silverman EK, Stoller JK, Trapnell B, Charlie S. Serum Proteins Associated with Emphysema Progression in Severe Alpha-1 Antitrypsin Deficiency. Chronic Obstr Pulm Dis. 2017 Jul 15;4(3):204-216. doi: 10.15326/jcopdf.4.3.2016.0180. PubMed PMID: 28848932; PubMed Central PMCID: PMC5556912.
  • Rivera-Garcia L, Hill-Spanik K, Berthrong S, Plante C. Tidal stage changes in structure and diversity of intertidal benthic diatom assemblages: A case study from two contrasting Charleston Harbor flats. Estuaries & Coasts. 2017. 41: 772-783 DOI: 10.1007/s12237-017-0312-4
  • Brown LN, Xing Y, Noble KV, Barth JL, Panganiban CH, Smythe NM, Bridges MC, Zhu J, Lang H. Macrophage-Mediated Glial Cell Elimination in the Postnatal Mouse Cochlea. Front Mol Neurosci. 2017 Dec 11;10:407. doi: 10.3389/fnmol.2017.00407. eCollection 2017. PubMed PMID: 29375297; PubMed Central PMCID: PMC5770652.
  • Zhou Y, Li P, Goodwin AJ, Cook JA, Halushka PV, Chang E, Fan H. Exosomes from Endothelial Progenitor Cells Improve the Outcome of a Murine Model of Sepsis. Mol Ther. 2018 Feb 27. pii: S1525-0016(18)30073-X. doi: 10.1016/j.ymthe.2018.02.020. [Epub ahead of print] PubMed PMID: 29599080
  • Panganiban CH, Barth JL, Darbelli L, Xing Y, Zhang J, Li H, Noble KV, Liu T, Brown LN, Schulte BA, Richard S, Lang H. Noise-induced dysregulation of Quaking RNA binding proteins contributes to auditory nerve demyelination and hearing loss. J Neurosci. 2018 March 7. 38 (10) 2551-2568; DOI: https://doi.org/10.1523/JNEUROSCI.2487-17.2018. PubMed PMID: 29437856. PMCID: PMC5858596

Contacts

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

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