The CoreMarketplace: UC Davis Genomics Shared Resource

UC Davis Medical Center - 4645 2nd Avenue, Research III, Room 3200D

Sacramento, CA 95817

United States

https://health.ucdavis.edu/cancer/research/sharedresources/ger.html

Google Maps Location

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Primary Contact:

John D. McPherson, Clifford Tepper

Last Updated: 05/30/2023

Facility RRID

RRID:SCR_023586

Facility Details

The Genomics Shared Resource, or GSR, provides expertise and comprehensive services to accomplish virtually every application of next- generation sequencing-based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single-cell sequencing and spatial transcriptomics services. The GSR also specializes in the development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides a wide range of additional services for translational and clinical genomics research.

Genomics Shared Resource is part of UC Davis Health Comprehensive Cancer Center.

Facility Policies

Services are offerred outside of University of California, Davis

Consulting is offerred outside of University of California, Davis

Services offered:

Facility Equipment

2100 Bioanalyzer Instrument

The 2100 Bioanalyzer system is an automated electrophoresis tool that provides precise analytical evaluation of various samples types in many workflows, including next generation sequencing (NGS), gene expression, biopharmaceutical, and gene editing research. Digital data is provided in a timely manner and delivers objective assessment of sizing, quantitation, integrity and purity from DNA, RNA, and proteins. Minimal sample volumes are required for an accurate result, and the data may be exported in a many different formats for ease-of-use. [Product Link]

RRID:SCR_018043

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Illumina MiSeq System

Access focused applications such as targeted resequencing, metagenomics, small genome sequencing, targeted gene expression profiling, and more. MiSeq reagents enable up to 15 Gb of output with 25 million sequencing reads and 2 Ã— 300 bp read lengths. [Product Link]

RRID:SCR_020134

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Thermo Scientific Nanodrop 1000 Spectrophotometer

The Thermo Scientific NanoDrop™ 1000 is a spectrophotometer that performs measuring of 1 ul samples with high accuracy and reproducibility. The full spectrum (220nm-750nm) spectrophotometer utilizes a patented sample retention technology that employs surface tension alone to hold the sample in place. This eliminates the need for cumbersome cuvettes and other sample containment devices and allows for clean up in seconds. In addition, the NanoDrop 1000 Spectrophotometer has the capability to measure highly concentrated samples without dilution (50X higher concentration than the samples measured by a standard cuvette spectrophotometer). [Product Link]

RRID:SCR_018035

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POLYTRON homogenizer

PowerServe Centro I1400 FTP Server

PowerWulf Compute Engine Computer Cluster

TissueRuptor homogenizer

UVP UV PCR Workstation

Covaris E220 Focused-ultrasonicator

Diagenode Bioruptor sonicator

Illumina DRAGEN Bio-IT Ultra-rapid Data Analysis Platform

Ultra-rapid NGS data analysis system

Life Technologies StepOnePlus Real-Time PCR System

Real-time PCR, qPCR

NanoString GeoMx Digital Spatial Profiler (DSP)

Spatial transcriptomics

NanoString GeoMx DSP Data Analysis Auxiliary Server

Computer server enabling simultaneous, multi-user data analyses

Sage Science Pippin Prep

ThermoFisher KingFisher Apex Automated Extraction Systems

ThermoFisher Qubit 2.0 Fluorometer

No additional equipment has been listed

Publications

Publications associated with this facility (Click To View):

1.) Shimoda M, Inagaki T, Davis RR, Merleev A, Tepper CG, Maverakis E, Izumiya Y (2023 Mar 26). KSHV uses viral IL6 to expand infected immunosuppressive macrophages. bioRxiv : the preprint server for biology, (), . . ID: 36945595.

2.) Yang G, Jena PK, Hu Y, Sheng L, Chen SY, Slupsky CM, Davis R, Tepper CG, Wan YY (2023 Feb 18). The essential roles of FXR in diet and age influenced metabolic changes and liver disease development: a multi-omics study. Biomarker research, 11(1), 20. . ID: 36803569.

3.) Alexandrou AT, Duan Y, Xu S, Tepper C, Fan M, Tang J, Berg J, Basheer W, Valicenti T, Wilson PF, Coleman MA, Vaughan AT, Fu L, Grdina DJ, Murley J, Wang A, Woloschak G, Li JJ (2022 Dec 22). PERIOD 2 regulates low-dose radioprotection via PER2/pGSK3β/β-catenin/Per2 loop. iScience, 25(12), 105546. . ID: 36465103.

4.) Woo XY, Srivastava A, Mack PC, Graber JH, Sanderson BJ, Lloyd MW, Chen M, Domanskyi S, Gandour-Edwards R, Tsai RA, Keck J, Cheng M, Bundy M, Jocoy EL, Riess JW, Holland W, Grubb SC, Peterson JG, Stafford GA, Paisie C, Neuhauser SB, Karuturi RKM, George J, Simons AK, Chavaree M, Tepper CG, Goodwin N, Airhart SD, Lara PN, Openshaw TH, Liu ET, Gandara DR, Bult CJ (2022 Nov 15). A Genomically and Clinically Annotated Patient-Derived Xenograft Resource for Preclinical Research in Non-Small Cell Lung Cancer. Cancer research, 82(22), 4126-4138. . ID: 36069866.

5.) Grimsrud KN, Davis RR, Tepper CG, Palmieri TL (2022 Sep 1). Pharmacogenetic Gene-Drug Associations in Pediatric Burn and Surgery Patients. Journal of burn care & research : official publication of the American Burn Association, 43(5), 987-996. . ID: 35639664.

6.) Campbell M, Chantarasrivong C, Yanagihashi Y, Inagaki T, Davis RR, Nakano K, Kumar A, Tepper CG, Izumiya Y (2022 Jul 27). KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin. Journal of virology, 96(14), e0056522. . ID: 35867573.

7.) Kumar A, Lyu Y, Yanagihashi Y, Chantarasrivong C, Majerciak V, Salemi M, Wang KH, Inagaki T, Chuang F, Davis RR, Tepper CG, Nakano K, Izumiya C, Shimoda M, Nakajima KI, Merleev A, Zheng ZM, Campbell M, Izumiya Y (2022 May 10). KSHV episome tethering sites on host chromosomes and regulation of latency-lytic switch by CHD4. Cell reports, 39(6), 110788. . ID: 35545047.

8.) Vinall R, Chen Q, Talbott G, Ramsamooj R, Dang A, Tepper CG, Borowsky A (2022 Jan 29). Use of RNA-Seq and a Transgenic Mouse Model to Identify Genes Which May Contribute to Mutant p53-Driven Prostate Cancer Initiation. Biology, 11(2), . . ID: 35205085.

9.) Lee AQ, Konishi H, Duong C, Yoshida S, Davis RR, Van Dyke JE, Ijiri M, McLaughlin B, Kim K, Li Y, Beckett L, Nitin N, McPherson JD, Tepper CG, Satake N (2022). A distinct subpopulation of leukemia initiating cells in acute precursor B lymphoblastic leukemia: quiescent phenotype and unique transcriptomic profile. Frontiers in oncology, 12(), 972323. . ID: 36212452.

10.) Wang J, Fite BZ, Kare AJ, Wu B, Raie M, Tumbale SK, Zhang N, Davis RR, Tepper CG, Aviran S, Newman AM, King DA, Ferrara KW (2022). Multiomic analysis for optimization of combined focal and immunotherapy protocols in murine pancreatic cancer. Theranostics, 12(18), 7884-7902. . ID: 36451859.

11.) Shimoda M, Lyu Y, Wang KH, Kumar A, Miura H, Meckler JF, Davis RR, Chantarasrivong C, Izumiya C, Tepper CG, Nakajima KI, Tuscano J, Barisone G, Izumiya Y (2021 Dec 2). KSHV transactivator-derived small peptide traps coactivators to attenuate MYC and inhibits leukemia and lymphoma cell growth. Communications biology, 4(1), 1330. . ID: 34857874.

12.) Liu C, Armstrong CM, Ning S, Yang JC, Lou W, Lombard AP, Zhao J, Wu CY, Yu A, Evans CP, Tepper CG, Li PK, Gao AC (2021 Sep). ARVib suppresses growth of advanced prostate cancer via inhibition of androgen receptor signaling. Oncogene, 40(35), 5379-5392. . ID: 34272475.

13.) Sun H, Cao S, Mashl RJ, Mo CK, Zaccaria S, Wendl MC, Davies SR, Bailey MH, Primeau TM, Hoog J, Mudd JL, Dean DA 2nd, Patidar R, Chen L, Wyczalkowski MA, Jayasinghe RG, Rodrigues FM, Terekhanova NV, Li Y, Lim KH, Wang-Gillam A, Van Tine BA, Ma CX, Aft R, Fuh KC, Schwarz JK, Zevallos JP, Puram SV, Dipersio JF, Davis-Dusenbery B, Ellis MJ, Lewis MT, Davies MA, Herlyn M, Fang B, Roth JA, Welm AL, Welm BE, Meric-Bernstam F, Chen F, Fields RC, Li S, Govindan R, Doroshow JH, Moscow JA, Evrard YA, Chuan (2021 Aug 24). Comprehensive characterization of 536 patient-derived xenograft models prioritizes candidatesfor targeted treatment. Nature communications, 12(1), 5086. . ID: 34429404.

14.) Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O (2021 May). Author Correction: Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nature genetics, 53(5), 761. . ID: 33608693.

15.) Fite BZ, Wang J, Kare AJ, Ilovitsh A, Chavez M, Ilovitsh T, Zhang N, Chen W, Robinson E, Zhang H, Kheirolomoom A, Silvestrini MT, Ingham ES, Mahakian LM, Tam SM, Davis RR, Tepper CG, Borowsky AD, Ferrara KW (2021 Jan 13). Immune modulation resulting from MR-guided high intensity focused ultrasound in a model of murine breast cancer. Scientific reports, 11(1), 927. . ID: 33441763.

16.) Woo XY, Giordano J, Srivastava A, Zhao ZM, Lloyd MW, de Bruijn R, Suh YS, Patidar R, Chen L, Scherer S, Bailey MH, Yang CH, Cortes-Sanchez E, Xi Y, Wang J, Wickramasinghe J, Kossenkov AV, Rebecca VW, Sun H, Mashl RJ, Davies SR, Jeon R, Frech C, Randjelovic J, Rosains J, Galimi F, Bertotti A, Lafferty A, O (2021 Jan). Conservation of copy number profiles during engraftment and passaging of patient-derived cancer xenografts. Nature genetics, 53(1), 86-99. . ID: 33414553.

17.) Lee AQ, Ijiri M, Rodriguez R, Gandour-Edwards R, Lee J, Tepper CG, Li Y, Beckett L, Lam K, Goodwin N, Satake N (2021). Novel Patient Metastatic Pleural Effusion-Derived Xenograft Model of Renal Medullary Carcinoma Demonstrates Therapeutic Efficacy of Sunitinib. Frontiers in oncology, 11(), 648097. . ID: 33842362.

18.) Chen H, Gotimer K, De Souza C, Tepper CG, Karnezis AN, Leiserowitz GS, Chien J, Smith LH (2020 Jun). Short-term organoid culture for drug sensitivity testing of high-grade serous carcinoma. Gynecologic oncology, 157(3), 783-792. . ID: 32253045.

Associations

ABRF

Association of Biomolecular Resource Facilities

Metadata

Links

All the links listed resolve to this core profile

https://coremarketplace.org/?FacilityID=1769
https://coremarketplace.org/RRID:SCR_023586

Institution

Institution ROR ID: https://ror.org/05rrcem69

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Keywords:

USEDit, ABRF, next generation sequencing based genomics research, gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services,

Resource Type:

core facility, access service resource, service resource

Citation:

University of California Davis Health Genomics Shared Resource Core Facility (RRID:SCR_023586)

UC Davis Genomics Shared Resource (Genomics / Genome Analysis and Technologies)

Primary Contact:

Facility RRID

Facility Details

Facility Policies

(To see more facility information, click the in the upper right)

Services offered:

Facility Equipment

(To see more facility information, click the in the upper right)

Publications

(To see more facility information, click the in the upper right)

Associations

ABRF

(To see more facility information, click the in the upper right)

Metadata

SciCrunch Data Imports (data maintained by https://scicrunch.org)

Facility Profile QR Code (links to this profile)

(To see more facility information, click the in the upper right)

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UC Davis Genomics Shared Resource

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