The Integrated Genomics Shared Resource in the Georgia Cancer Center houses a complete lllumina NextGen Sequencing Facility including both HiSeq, MiSeq, and NextSeq 500 instruments.
Expertise for performing DNA-Seq, RNA-Seq, Chip-Seq, Methyl-Seq and single cell sequencing is available. Microarray resources offer the Affymetrix Platform in order to facilitate exon-specific, oligonucleotide and genome-wide arrays. Bioinformatics support is available for data analysis for both sequencing and microarray data. Partek Genomics Suite and Ingenuity Pathways Analysis Softwares are available for analyses of genomic data.
Please note that pricing is subject to charges of the suppliers. All services are booked through iLAB
qPCR measurement with the addition of the Illumina HiSeq 2500 and NextSeq 500 offers single-read, paired-end, and multiplex sequencing. The Resource also offers library preparation services for DNA-seq, RNA-seq, CHIP-seq and other standard sequencing libraries.
Microarrays are performed using the Affymetrix® Platform. Gene expression arrays that provide estimates of mRNA levels in tumors have given rise to exon-specific arrays that can identify both gene expression levels, alternative splicing events and mRNA processing alterations. Oligonucleotide arrays are also being used to interrogate single nucleotide polymorphisms (SNPs) throughout the genome for linkage and association studies, and these have been adapted to quantify copy number abnormalities and loss of heterozygosity (LOH) events. To identify as yet unknown transcripts, tiling arrays across the genome have been developed. Global DNA methylation changes can be detected using array platforms. Additionally, it has now become possible to identify DNA-protein interactions using ChIP-on-Chip protocols. With all of these capabilities becoming routine in genomics laboratories, the idea of a systematic characterization of the sum of genetic events that give rise to a cancer cell is rapidly becoming a reality.
The gene expression arrays that provide estimates of mRNA levels in tumors have given rise to exon-specific arrays that can identify both gene expression levels, alternative splicing events and mRNA and miRNA processing alterations. Oligonucleotide arrays are also used to interrogate single nucleotide polymorphisms (SNPs) throughout the genome for linkage and association studies, and these have been adapted to quantify copy number abnormalities and loss of heterozygosity (LOH) events.
Genome-wide tiling arrays have been developed to identify as yet unknown transcripts. Global DNA methylation changes can be detected using array platforms. High-resolution copy-number and LOH for human and mouse can also be performed, as well as genome-wide association studies. Additionally, it has now become possible to identify DNA-protein interactions using chromatin immunoprecipitation (ChIP) on Chip protocols. With all of these capabilities becoming routine in genomics laboratories, the idea of a systematic characterization of the sum of genetic events that give rise to a cancer cell is rapidly becoming a reality.
Software, training and support is also available for researchers to enable them to analyze large data sets and obtain meaningful results from their experiments. A large number of state-of-the-art programs are available to afford analyses of different data types, and expertise is available to implement and advise on their usage.
(NOTE: Images reproduced with permission of Affymetrix ®, Inc. Content from Affymetrix ®. Affymetrix ® and all its other trademarks are the property of Affymetrix ®, Inc.)
The Resource aims to provide Georgia Cancer Center researchers access to microarray technology and bioinformatics at an affordable cost.* The Resource offers consultation, training and educational seminars on:
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.
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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.
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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.
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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
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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.
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