Molecular Analytics Core

Molecular Analytics Core data visualizations

The mission of the core is to provide MUSC and other regional investigators with expertise, instrumentation, training, and services for a range of molecular technologies. The core currently offers Bioanalyzer service for qualitative analysis of eukaryotic total RNA and quantitative analysis of DNA libraries. Several instruments are available to users, including qPCR, PCR, NanoDrop, microplate reader, and Qubit fluorometers. Following certification of training, users are free to schedule their use at their convenience. The core also offers bioinformatic analysis in support of bulk RNA-seq data analysis and other miscellaneous applications (database mining, cloning design, etc.) For RNA-seq projects, the core can access raw data from providers, run data analysis pipelines, securely store the data until publication, and assist users with submission of project data to public archives.

Publication Acknowledgement

The Molecular Analytics Core is supported by NIGMS GM103499, MUSC’s Office of the Vice President for Research, and the MUSC Department of Regenerative Medicine and Cell Biology.

Pandey, J. P., Nietert, P. J., Kothera, R. T., Barnes, L. L., & Bennett, D. A. (2021). Interactive Effects of HLA and GM Alleles on the Development of Alzheimer Disease. Neurology. Genetics, 7(2), e565. https://doi.org/10.1212/NXG.0000000000000565

Panganiban, C. H., Barth, J. L., Tan, J., Noble, K. V., McClaskey, C. M., Howard, B. A., Jafri, S. H., Dias, J. W., Harris, K. C., & Lang, H. (2022). Two distinct types of nodes of Ranvier support auditory nerve function in the mouse cochlea. Glia, 70(4), 768–791. https://doi.org/10.1002/glia.24138

Fu, X., Cheng, D., Luo, Z., Wagner, A., Fitting, S., Cong, X., Xu, W., Maas, K., Wan, Z., Zhu, J., Zhou, Z., Stoops, W. W., McRae-Clark, A., & Jiang, W. (2022). Oral Enrichment of Streptococcus and its Role in Systemic Inflammation Related to Monocyte Activation in Humans with Cocaine Use Disorder. Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology, 17(1-2), 305–317. https://doi.org/10.1007/s11481-021-10007-6

Heslop, J. A., Pournasr, B., Liu, J. T., & Duncan, S. A. (2021). GATA6 defines endoderm fate by controlling chromatin accessibility during differentiation of human-induced pluripotent stem cells. Cell reports, 35(7), 109145. https://doi.org/10.1016/j.celrep.2021.109145

Gao, X., Qin, S., Wu, Y., Chu, C., Jiang, B., Johnson, R. H., Kuang, D., Zhang, J., Wang, X., Mehta, A., Tew, K. D., Leone, G. W., Yu, X. Z., & Wang, H. (2021). Nuclear PFKP promotes CXCR4-dependent infiltration by T cell acute lymphoblastic leukemia. The Journal of clinical investigation, 131(16), e143119. https://doi.org/10.1172/JCI143119

Li, P., Wu, Y., Hamlett, E. D., Goodwin, A. J., Halushka, P. V., Carroll, S. L., Liu, M., & Fan, H. (2022). Suppression of Fli-1 protects against pericyte loss and cognitive deficits in Alzheimer's disease. Molecular therapy : the journal of the American Society of Gene Therapy, 30(4), 1451–1464. https://doi.org/10.1016/j.ymthe.2022.01.023

Casazza, J. P., Cale, E. M., Narpala, S., Yamshchikov, G. V., Coates, E. E., Hendel, C. S., Novik, L., Holman, L. A., Widge, A. T., Apte, P., Gordon, I., Gaudinski, M. R., Conan-Cibotti, M., Lin, B. C., Nason, M. C., Trofymenko, O., Telscher, S., Plummer, S. H., Wycuff, D., Adams, W. C., … VRC 603 Study Team (2022). Safety and tolerability of AAV8 delivery of a broadly neutralizing antibody in adults living with HIV: a phase 1, dose-escalation trial. Nature medicine, 28(5), 1022–1030. https://doi.org/10.1038/s41591-022-01762-x

Pandey J. P. (2022). IgG3 constant region GM (γ marker) allotypes could influence the neutralizing potency of anti-SARS-CoV-2 monoclonal antibodies. Proceedings of the National Academy of Sciences of the United States of America, 119(6), e2119380119. https://doi.org/10.1073/pnas.2119380119

Bowers, R. R., Andrade, M. F., Jones, C. M., White-Gilbertson, S., Voelkel-Johnson, C., & Delaney, J. R. (2022). Autophagy modulating therapeutics inhibit ovarian cancer colony generation by polyploid giant cancer cells (PGCCs). BMC cancer, 22(1), 410. https://doi.org/10.1186/s12885-022-09503-6

Luo, Z., Li, M., Li, T. W., Lv, Z., Ye, Z., Cisneros, W. J., Zhang, J., Yuan, L., Hultquist, J. F., Migueles, S. A., Huang, L., Zhu, J., & Jiang, W. (2022). Differential Expression of CREM/ICER Isoforms Is Associated with the Spontaneous Control of HIV Infection. mBio, 13(1), e0197921. https://doi.org/10.1128/mbio.01979-21

James, W. A., Ogunrinde, E., Wan, Z., Kamen, D. L., Oates, J., Gilkeson, G. S., & Jiang, W. (2022). A Distinct Plasma Microbiome But Not Gut Microbiome in Patients With Systemic Lupus Erythematosus Compared to Healthy Individuals. The Journal of rheumatology, 49(6), 592–597. https://doi.org/10.3899/jrheum.210952

Luo, Z., Health, S. L., Li, M., Yang, H., Wu, Y., Collins, M., Deeks, S. G., Martin, J. N., Scott, A., & Jiang, W. (2022). Variation in blood microbial lipopolysaccharide (LPS) contributes to immune reconstitution in response to suppressive antiretroviral therapy in HIV. EBioMedicine, 80, 104037. https://doi.org/10.1016/j.ebiom.2022.104037

Hathaway-Schrader, J. D., Norton, D., Hastings, K., Doonan, B. P., Fritz, S. T., Bethard, J. R., Blum, J. S., & Haque, A. (2022). GILT Expression in Human Melanoma Cells Enhances Generation of Antigenic Peptides for HLA Class II-Mediated Immune Recognition. International journal of molecular sciences, 23(3), 1066. https://doi.org/10.3390/ijms23031066

Xiong, W., Gao, X., Zhang, T., Jiang, B., Hu, M. M., Bu, X., Gao, Y., Zhang, L. Z., Xiao, B. L., He, C., Sun, Y., Li, H., Shi, J., Xiao, X., Xiang, B., Xie, C., Chen, G., Zhang, H., Wei, W., Freeman, G. J., … Zhang, J. (2022). USP8 inhibition reshapes an inflamed tumor microenvironment that potentiates the immunotherapy. Nature communications, 13(1), 1700. https://doi.org/10.1038/s41467-022-29401-6

Heslop, J. A., Pournasr, B., & Duncan, S. A. (2022). Chromatin remodeling is restricted by transient GATA6 binding during iPSC differentiation to definitive endoderm. iScience, 25(5), 104300. https://doi.org/10.1016/j.isci.2022.104300

Glover, J. S., Ticer, T. D., & Engevik, M. A. (2022). Characterizing the mucin-degrading capacity of the human gut microbiota. Scientific reports, 12(1), 8456. https://doi.org/10.1038/s41598-022-11819-z

Glover, J. S., Browning, B. D., Ticer, T. D., Engevik, A. C., & Engevik, M. A. (2022). Acinetobacter calcoaceticus is Well Adapted to Withstand Intestinal Stressors and Modulate the Gut Epithelium. Frontiers in physiology, 13, 880024. https://doi.org/10.3389/fphys.2022.880024

Fan, J., Liu, J., Liu, J., Angel, P. M., Drake, R. R., Wu, Y., Fan, H., Koutalos, Y., & Crosson, C. E. (2022). Sphingomyelinases in retinas and optic nerve heads: Effects of ocular hypertension and ischemia. Experimental eye research, 224, 109250. https://doi.org/10.1016/j.exer.2022.109250

Ning, W., Xu, W., Cong, X., Fan, H., Gilkeson, G., Wu, X., Hughes, H., & Jiang, W. (2022). COVID-19 mRNA vaccine BNT162b2 induces autoantibodies against type I interferons in a healthy woman. Journal of autoimmunity, 132, 102896. https://doi.org/10.1016/j.jaut.2022.102896

Wu, Y., Li, P., Liu, L., Goodwin, A. J., Halushka, P. V., Hirose, T., Nakagawa, S., Zhou, J., Liu, M., & Fan, H. (2022). lncRNA Neat1 regulates neuronal dysfunction post-sepsis via stabilization of hemoglobin subunit beta. Molecular therapy : the journal of the American Society of Gene Therapy, 30(7), 2618–2632. https://doi.org/10.1016/j.ymthe.2022.03.011

Li, P., Wu, Y., Hamlett, E. D., Goodwin, A. J., Halushka, P. V., Carroll, S. L., Liu, M., & Fan, H. (2022). Suppression of Fli-1 protects against pericyte loss and cognitive deficits in Alzheimer's disease. Molecular therapy : the journal of the American Society of Gene Therapy, 30(4), 1451–1464. https://doi.org/10.1016/j.ymthe.2022.01.023

Bowers, R. R., Jones, C. M., Paz, E. A., Barrows, J. K., Armeson, K. E., Long, D. T., & Delaney, J. R. (2022). SWAN pathway-network identification of common aneuploidy-based oncogenic drivers. Nucleic acids research, 50(7), 3673–3692. https://doi.org/10.1093/nar/gkac200

Bowers, R. R., Andrade, M. F., Jones, C. M., White-Gilbertson, S., Voelkel-Johnson, C., & Delaney, J. R. (2022). Autophagy modulating therapeutics inhibit ovarian cancer colony generation by polyploid giant cancer cells (PGCCs). BMC cancer, 22(1), 410. https://doi.org/10.1186/s12885-022-09503-6

White-Gilbertson, S., Lu, P., Esobi, I., Echesabal-Chen, J., Mulholland, P. J., Gooz, M., Ogretmen, B., Stamatikos, A., & Voelkel-Johnson, C. (2022). Polyploid giant cancer cells are dependent on cholesterol for progeny formation through amitotic division. Scientific reports, 12(1), 8971. https://doi.org/10.1038/s41598-022-12705-4

Luo, Z., Health, S. L., Li, M., Yang, H., Wu, Y., Collins, M., Deeks, S. G., Martin, J. N., Scott, A., & Jiang, W. (2022). Variation in blood microbial lipopolysaccharide (LPS) contributes to immune reconstitution in response to suppressive antiretroviral therapy in HIV. EBioMedicine, 80, 104037. https://doi.org/10.1016/j.ebiom.2022.104037

Ning, W., Cheng, D., Howe, P. H., Bian, C., Kamen, D. L., Luo, Z., Fu, X., Ogunrinde, E., Yang, L., Wang, X., Li, Q. Z., Oates, J., Zhang, W., White, D., Wan, Z., Gilkeson, G. S., & Jiang, W. (2022). Staphylococcus aureus peptidoglycan (PGN) induces pathogenic autoantibody production via autoreactive B cell receptor clonal selection, implications in systemic lupus erythematosus. Journal of autoimmunity, 131, 102860. https://doi.org/10.1016/j.jaut.2022.102860

Wang, X., Zhou, Z., Turner, D., Lilly, M., Ou, T., & Jiang, W. (2022). Differential Circulating Fungal Microbiome in Prostate Cancer Patients Compared to Healthy Control Individuals. Journal of immunology research, 2022, 2574964. https://doi.org/10.1155/2022/2574964

Anderson, E. M., Tsvetkov, E., Galante, A., DeVries, D., McCue, L. M., Wood, D., Barry, S., Berto, S., Lavin, A., Taniguchi, M., & Cowan, C. W. (2023). Epigenetic function during heroin self-administration controls future relapse-associated behavior in a cell type-specific manner. Proceedings of the National Academy of Sciences of the United States of America, 120(7), e2210953120. https://doi.org/10.1073/pnas.2210953120

Hughes, B. W., Siemsen, B. M., Tsvetkov, E., Berto, S., Kumar, J., Cornbrooks, R. G., Akiki, R. M., Cho, J. Y., Carter, J. S., Snyder, K. K., Assali, A., Scofield, M. D., Cowan, C. W., & Taniguchi, M. (2023). NPAS4 in the medial prefrontal cortex mediates chronic social defeat stress-induced anhedonia-like behavior and reductions in excitatory synapses. eLife, 12, e75631. https://doi.org/10.7554/eLife.75631

Dupuis, L. E., Evins, S. E., Abell, M. C., Blakley, M. E., Horkey, S. L., Barth, J. L., & Kern, C. B. (2023). Increased Proteoglycanases in Pulmonary Valves after Birth Correlate with Extracellular Matrix Maturation and Valve Sculpting. Journal of cardiovascular development and disease, 10(1), 27. https://doi.org/10.3390/jcdd10010027