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

Contact Us

Integrated Genomics

Eiko Kitamura, PhD

(706) 721-5471

ekitamura@augusta.edu


Sam Chang, PhD

(706) 446-5528

chchang@augusta.edu

Next Generation Sequencing

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.

Next Generation Service Pricing (Link)

Chromium Controller 10X

Equipment/infrastructure

  • 10X Genomics Chromium Controller
  • Agilent ® 2100 Bioanalyzer
  • Agilent ® 2200 TapeStation
  • NanoDrop 1000
  • QuBit Fluorometer
  • Illumina HiSeq 2500 (Rapid & Hi-Throughput Modes)
  • Illumina Miseq
  • Illumna NextSeq 500
  • cBot Cluster Generation System
  • Applied Biosystems GeneAmp 9700 Thermocycler
  • Covaris

APPLICATIONS

  • DNA Sequencing
  • Gene Regulation Analysis
  • Sequencing-Based Transcriptome Analysis
  • SNP Discovery and Structural Variation Analysis
  • Cytogenetic Analysis
  • DNA-Protein Interaction Analysis (ChIP-Seq)
  • Sequencing-Based Methylation Analysis
  • Chromium Single Cell Gene Expression

DATA ANALYSIS

  • Partek Genomics Suite
  • TrueSeqEnrichment Analysis Tool
  • BWA Alignment
  • Bowtie Alignment
  • GATKx
  • VarScan2
  • Tophat2 & Cufflinks (RNAseq analysis tool recommended by illumina)
  • GSNAP & GMAP
  • RSEM (de novo RNA assembly)
  • ExomeCNV
  • FusionMap
  • Tools for DNA-Seq, RNA-Seq and CHIP-Seq analyses
  • Loupe Cell Browser for Single Cell Gene Expression

Affymetrix Technology

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.)

Array Pricing for Affymetrix Technology (Link)

 

EQUIPMENT / INFRASTRUCTURE

  • Affymetrix ® GeneChip Scanner 3000 7G Plus
  • Affymetrix ® Hybridization Oven 640
  • Affymetrix ® Fluidics Station 450 (x2)

DATA ANALYSIS

  • Affymetrix ® Genotyping Console
  • Affymetrix ® Expression Console

BIOINFORMATICS AND SUPPORT

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:

  • analysis of microarray data
  • programs designed to analyze large data sets
  • gene expression
  • the roles of DNA sequence variation in the genome

Publications

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.

PUBLICATIONS RESULTING FROM NGS RESOURCE USE

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.

 

PUBLICATIONS RESULTING FROM MICROARRAY AND INGENUITY PATHWAY ANALYSIS  RESOURCE USE

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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