The Integrated Genomics Shared Resource in the Georgia Cancer Center offer cutting edge technologies for DNA and RNA sequencing as well as spatial transcriptomic.
We offer a wide range of services from sample processing from both fresh and frozen, as well as fixed cells or tissues to library preparation and next-generation sequencing (NGS) for bulk DNA/RNA sequencing and single-cell/nuclei sequencing. For single-cell studies, we are equipped with the Chromium X system from 10X Genomics. Our sequencing capabilities include the Illumina Novaseq6000 and NextSeq 500. We recently introduce single cell spatial transcriptomics with CosMx SMI platform been able to provide support to investigator that are focusing on single cell in tissue in a specific microenvironment. We are also equipped with CytAssit instrument from 10X genomics for VISIUM spatial transcriptomic. For nucleic acid and protein extraction we are equipped with QIAConnect from Qiagen.
Please note that pricing is subject to charges of the suppliers.
Qiagen |Sample Purification
QIAcube Connect is designed to perform fully automated purification of nucleic acids and proteins in molecular biology applications. The system is intended for use by professional users trained in molecular biological techniques and the operation of QIAcube Connect.
10X Genomics |Single Cell & Spatial Transcriptomic Platform
The Chromium X Series instrument enables seamless scaling from pilot experiments through million-cell studies, and offers compatibility with an expanding range of Chromium Single Cell applications.
Nanostring | Single cell Spatial Transcriptomic Platform
CosMx SMI is the first high-plex in situ analysis platform to provide spatial multiomics with formalin-fixed paraffin-embedded (FFPE) and fresh frozen (FF) tissue samples at cellular and subcellular resolution.
illumina | Next Generation Sequencing
The NovaSeq 6000 system performs whole-genome sequencing efficiently and cost-effectively. Its tunable output generates up to 6 Tb and 20B single reads in dual flow cell mode with streamlined workflows.
Quality control equipment
Including Agilent 2100 bioanalyzer, Agielnt 2200 Tapstation, Qubit fluorometer and NanoDrop 1000.
Researchers who use Georgia Cancer Center shared resources, including the Integrated Genomics Resource, must include recognition of Cancer Center membership on all cancer-related academic papers, grants, journal articles, poster sessions and/or abstracts.
John K Cowell, Haiyang Qin, Chang-Sheng Chang, Eiko Kitamura, Mingqiang Ren. A model of BCR-FGFR1 driven human AML in immunocompromised mice. British Journal of Haematology., 2016, 175(3): 542-545
Drewry M, Helwa I, Allingham RR, Hauser MA, Liu Y. (2016). miRNA profile in three different normal human ocular tissues by miRNA-seq. Invest Ophthalmol vis Sci. 2016, 1;57(8):3731-9
Pathania R, Ramachandran S, Mariappan G, Thakur P, Shi H, Choi JH, Manicassamy S, Kolhe R, Prasad PD, Sharma S, Lokeshwar BL, Ganapathy V, Thangaraju M. (2016). Combined Inhibition of DNMT and HDAC blocks the tumorigenicity of cancer stem-like cells and attenuates mammary tumor growth. Cancer Res., 2016, 1;76(11):3224-35.
Zhu X, Hu T, Ho MH, Wang Y, Yu M, Patel N, Pi W, Choi JH, Xu H, Kutlar F, Ganapathy V, Kutlar A, Tuan D. Hydroxyurea differentially modulates activator and repressors of γ-globin gene in erythroblasts of responsive and non-responsive patients with sickle cell disease in correlation with Index of Hydroxyurea Responsiveness. Haematologica, 2017 Dec; 102(12):1995-2004.
Hu T, Chong Y, Lu S, Wang R, Qin H, Silva J, Kitamura E, Chang C-S, Hawthorn L, Cowell JK. MicroRNA339 promotes development of Stem Cell Leukemia/Lymphoma syndrome through downregulation of the BCL2L11 and BAX pro-apoptotic genes. Cancer Research, 2018 Apr; 1;78(13):3522-3531
Khaled ML, Bykhovskaya Y, Yablonski SER, Li H, Drewry MD, Aboobakar IF, Estes A, Gao XR, Stamer WD, Xu H, Allingham RR, Hauser MA, Rabinowitz YS, Liu Y. Differential Expression of Coding and Long Noncoding RNAs in Keratoconus-Affected Corneas. Invest Ophthalmol Vis Sci., 2018 Jun;59(7):2717-2728.
Hu T, Chong Y, Cai B, Liu Y, Lu S, Cowell JK. DNA methyltransferase 1-mediated CpG methylation of the miR-150-5p promoter contributes to fibroblast growth factor receptor 1-driven leukemogenesis. J. Biol Chem., 2019 Oct RA119.010144.
Chang C-S, Kitamura E, Johnson J, Bollag R, Hawthorn L. Genomic analysis of racial differences in triple negative breast cancer. Genomics, 2019 Dec; 111(6):1529-1542.
Silva J, Chang C-S, Hu T, Qin H, Kitamura E, Hawthorn L, Ren M, Cowell JK. Distinct signaling programs associated with progression of FGFR1 driven leukemia in a mouse model of stem cell leukemia lymphoma syndrome. Genomics, 2019 Dec; 111(6):1566-1573.
Hu T, Liu Y, Lu S, Cai B, Qin H, Chang C-S, Ren M, Cowell JK. Critical individual roles of the BCR and FGFR1 kinase domains in BCR-FGFR1-driven stem cell leukemia/lymphoma syndrome. Int. J. Cancer, 2019 Sep 16. doi: 10.1002/ijc.32665.
Kitamura E, Cowell JK, Chang C-S, Hawthorn L. Mutational analysis of genes mapping to chromosome 16q loss in Wilms tumors reveals link to cilia-related genes and pathways. Gene & Cancer, 2020 Oct 6; 6;11 (3-4):137-153.
Liu Y, Cai B, Chong Y, Zhang H, Kemp C-A, Lu S, Chang C-S, Ren M, Cowell JK, Hu T. Downregulation of PUMA underlies resistance to FGFR1 inhibitors in the stem cell leukemia/Lymphoma syndrome. Cell Death Dis, 2020 Oct 20; 11(10):884.
Yu M, Guo G, Huang L, Deng L, Chang C-S, Achyut BR, Canning M, Xu N, Arbab AS, Bollag R, Rodriguez PC, Mellor AL, Shi H, Munn DH, Cui Y. CD73 on cancer-associated fibroblasts enhanced by the A2B-mediated feedforward circuit enforces an immune checkpoint. Nat Commun, 2020 Jan 24;11(1):515. Doi: 10.1038/s41467-019-14060-x.
Ding ZC, Shi H, Aboelella NS, Fesenkova K, Park EJ, Liu Z, Pei L, Li J, McIndoe RA, Xu H, Piazza GA, Blazar BR, Munn DH, Zhou G. Persistent STAT5 activation reprograms the epigenetic landscape in CD4+ T cells to drive polyfunctionality and antitumor immunity. Sci Immunol., 2020 Oct 30;5(52) :eaba5962. doi: 10.1126/sciimmunol.aba5962.
Brown ME, Montgomery ML, Kamath MM, Nicholas S, Liu Y, Karamichos D, Fuller KK. A novel 3D culture model of fungal keratitis to explore host-pathogen interactions within the stromal environment. Exp Eye Res., 2021 Apr 15;207:108581. doi: 10.1016/j.exer.2021.108581.
Sharma MD, Pacholczyk R, Shi H, Berrong ZJ, Zakharia Y, Greco A, Chang CS, Eathiraj S, Kennedy E, Cash T, Bollag RJ, Kolhe R, Sadek R, McGaha TL, Rodriguez P, Mandula J, Blazar BR, Johnson TS, Munn DH. Inhibition of the BTK-IDO-mTOR axis promotes differentiation of monocyte-lineage dendritic cells and enhances anti-tumor T cell immunity. Immunity. 2021 Oct 12;54(10):2354-2371.e8. doi: 10.1016/j.immuni.2021.09.005. Epub 2021 Oct 5.
Ma Z, Hu X, ding HF, Zhang M, Huo Y, Dong Z. Single-nucleus transcriptional profiling of chronic kidney disease after cisplatin nephrotoxicity. Am J Pathol. 2022 Apr;192(4):613-628. doi: 10.1016/j.ajpath.2021.12.012. Epub 2022 Jan 31.
Li X, Gracilla D, Cai L, Zhang M, Yu X, Chen X, Zhang J, Long X, Ding HF, Yan C. ATF3 promotes the serine synthesis pathway and tumor growth under dietary serine restriction. Cell Rep. 2021 Sep 21;36(12):109706. doi: 10.1016/j.celrep.2021.109706.
Parker E, Khayrullin A, Kent A, Mendhe B, Youssef El, Baradie KB, Yu K, Pihkala J, Liu Y, McGee-Lawrence M, Johnson M, Chen J, Hamrick M. Hindlimb immobilization increases IL-1beta and Cdkn2a expression in skeletal muscle fibro-adipogenic progenitor cells: A link between senescence and muscle disuse atrophy. Front Cell Dev Biol. 2022 Jan 3;9:790437. doi: 10.3389/fcell.2021.790437. eCollection 2021.
Bhagirath D, Liston M, Akoto T, Lui B, Bensing BA, Sharma A, Saini S. Novel non-invasive markers for detecting therapy induced neuroendocrine differentiation in castration-resistant prostate cancer patients. Sci Rep. 2021 Apr 15;11(1):8279. doi: 10.1038/s41598-021-87441-2.
Baohuan Cai, Yun Liu, Yating Chong, Stephanie Fay Mori, Atsuko Matsunaga, Hualei Zhang, Xuexiu Fang, Chang-Sheng Chang, John K Cowell, Tianxiang Hu. A truncated derivative of FGFR1 kinase cooperates with FLT3 and KIT to transform hematopoietic stem cells in syndromic and de novo AML. Mol Cancer. 2022 Jul 29;21(1):156. doi: 10.1186/s12943-022-01628-3.
Hualei Zhang, Baohuan Cai, Yun Liu, Yating Chong, Atsuko Matsunaga, Stephanie Fay Mori, Xuexiu Fang, Eiko Kitamura, Chang-Sheng Chang, Ping Wang, John K Cowell, Tianxiang Hu. RHOA-regulated IGFBP2 promotes invasion and drives progression of BCR-ABL1 chronic myeloid leukemia. Haematologica. 2023 Jan 1;108(1):122-134. doi: 10.3324/haematol.2022.280757.
Zhao E, Ding J, Xia Y, Liu M, Ye B, Choi JH, Yan C, Dong Z, Huang S, Zha Y, Yang L, Cui H, Ding HF. KDM4C and ATF4 cooperate in transcriptional control of amino acid metabolism. Cell Rep., 2016, 26;14(3):506-519.
Khayrullin A, Smith L, Mistry D, Dukes A, Pan YA, Hamrick MW. Chronic alcohol exposure induces muscle atrophy (myopathy) in zebrafish and alters the expression of microRNAs targeting the Notch pathway in skeletal muscle. Biochem Biophys Res Commun., 2016, 21;479(3):590-595.
Davis C, Dukes A, Drewry M, Helwa I, Johnson MH, Isales CM, Hill WD, Liu Y, Shi X, Fulzele S, Hamrick MW. MicroRNA-183-5p increases with age in bone-derived extracellular vesicles, suppresses bone marrow stromal (stem) cell proliferation, and induces stem cell senescence. Tissue Eng. PartA., 2017, 23(21-22):1231-1240.
Ouzounova M, Lee E, Piranlioglu R, El Andaloussi A, Kolhe R, Demirci MF, Marasco D, Asm I, Chadli A, Hassan KA, Thangaraju M, Zhou G, Arbab AS, Cowell JK, Korkaya H. Monocytic and granulocytic myeloid drived suppressor cells differentially regulate spatiotemporal tumor plasticity during metastatic cascade. Nat commun, 2017, 6;8:14979.
Alwhaibi A, Gao F, Artham S, Hsia BM, Mondal A, Kolhe R, Somanath PR. Modulation in the microRNA repertoire is responsible for the stage-specific effects of Akt suppression on murine neuroendocrine prostate cancer. Heliyon, 2018, 17;4(9):e00796.
Ju C, Li Y, Shen Y, Liu Y, Cai J, Liu N, Ma G, Tang Y. Transplantation of Cardiac Mesenchymal Stem Cell-Derived Exosomes for Angiogenesis. J Cardiovasc Transl Res., 2018, 11(5):429-437.
Ko EK, Chorich LP, Sullivan ME, Cameron RS, Layman LC. JAK/STAT signaling pathway gene expression is reduced following Nelf knockdown in GnRH neurons. Mol Cell Endocrinol, 2018, 15;470:151-159.
Hu T, Chong Y, Qin H, Kitamura E, Chang C-S, Silva J, Ren M, Cowell JK. The miR-17/92 cluster is involved in the molecular etiology of the SCLL syndrome driven by the BCR-FGFR1 chimeric kinase. Oncogene, 2018 Apr; 37(14), 1926-1938.
Artham S, Gao F, Verma A, Alwhaibi A, Sabbineni H, Hafez S, Ergul A, Somanath RP. Endothelial stromelysin1 regulation by the forkhead box-O transcription factors is crucial in the exudative phase of acute lung injury. Pharmacol. Res., 2019 Mar 141:249-263.
Piranlioglu R, Lee E, Ouzounova M, Bollag RJ, Vinyard AH, Arbab AS, Marasco D, Guzel M, Cowell JK, Thangaraju M, Chadli A, Hassan KA, Wicha MS, Celis E, Korkaya H. Primary tumor-induced immunity eradicates disseminated tumor cells in syngeneic mouse model. Nat Commun., 2019 Mar 29;10(1):1430
Ajith A, Portik-Dobos V, Nguyen-Lefebvre AT, Callaway C, Horuzsko DD, Kapoor R, Zayas C, Maenaka K, Mulloy LL, Horuzsko A. HLA-G dimer targets Granzyme B pathway to prolong human renal allograft survival. FASEB J., 2019 Apr;33(4):5220-5236.
Eisa NH, Jilani Y, Kainth K, Redd P, Lu S, Bougrine O, Abdul Sater H, Patwardhan CA, Shull A, Shi H, Liu K, Elsherbiny NM, Eissa LA, El-Shishtawy MM, Horuzsko A, Bollag R, Maihle N, Roig J, Korkaya H, Cowell JK, Chadli A. The co-chaperone UNC45A is essential for the expression of mitotic kinase NEK7 and tumorigenesis. J Biol Chem., 2019 Apr 5;294(14):5246-5260.
Silva J, Hawthorn L, Cowell JK. Inactivation of Lgi1 in murine neuronal precursor cells leads to dysregulation of axon guidance pathways. Genomics., 2019 Jul. S0888-7543(19)30015-1
Xia Y, Ye B, Ding J, Yu Y, Alptekin A, Thangaraju M, Prasad PD, Ding ZC, Park EJ, Choi JH, Bao B, Fiehn O, Yan C, Dong Z, Zha Y, Ding HF. Metabolic reprogramming by MYCN confers dependence on the serine-glycine-one-carbon biosynthetic pathway. Cancer Res., 2019 Aug 1;79(15):3837-3850.
Alptekin A, Ye B, Yu Y, Poole CJ, van Riggelen J, Zha Y, Ding HF. Glycine decarboxylase is a transcriptional target of MYCN required for neuroblastoma cell proliferation and tumorigenicity. Oncogene, 2019 Aug 23.
Elashiry M, Elashiry MM, Elsayed R, Rajendran M, Auersvald C, Zeitoun R, Rashi MH, Ara R, Meghil MM, Liu Y, Arbab AS, Arce RM, Hamrick MW, Elsalanty M, Brendan M, Pacholczyk R, Cutler CW. Dendritic cell derived exosomes loaded with immunoregulatory cargo reprogram local immune responses and inhibit degenerative bone disease in vivo. J Extracell Vesicles., 2020 Aug 7. Doi: 10.1080/20013078.2020.1795362.
Dalton S, Smith K, Singh K, Kaiser H, Kohle R, Mondal AK, Khayrullin A, Isales CM, Hamrick MW, Hill WD, Fulzele S. Accumulation of kynurenine elevates oxidative stress and alters microRNA profile in human bone marrow stromal cells. Exp Gerontol., 2020 Feb: 130: 110800
Ding Z-C, Aboelella NS, Bryan L, Shi H, Zhou G. The monocytes that repopulate in mice after cyclophosphamide treatment acquire a neutrophil precursor gene signature and immunosuppressive activity. Front Immunol., 2021 Jan 25. Doi:10.3389/fimmu.2020.594540
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