The CoreMarketplace: UHCC Genomics and Bioinformatics Shared Resource

The UHCC GBSR is a Shared Resource at the University of Hawaii Cancer Center. The genomic analysis services offered are: (1) DNA/RNA isolation, plating, and quality analysis, (2) Custom genotyping, (3) Real-Time qPCR-based gene expression, copy number and methylation assays, (4) Pyrosequencing, (5) Affymetrix and Illumina microarray-based assays, (6) Next Generation Sequencing on NextSeq500, iSeq100, (7) NanoString nCounter analysis, and (8) Consultation. We also offer bioinformatic analysis services for various omics data.

Facility Policies

Services are offerred outside of University of Hawaii at Manoa

Consulting is offerred outside of University of Hawaii at Manoa

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

Services offered:

10x Genomics

Assays and Measurements

Computational - Bioinformatics

Copy Number Variation (CNV)

Nucleic Acid Extraction

Sequencing - DNA Sequencing

Sequencing - Next Generation Sequencing (NGS)

Sequencing - Pyrosequencing

Facility Equipment

Illumina iScan System
Illumina NextSeq 500 NGS System
Illumina iSeq 100 NGS System
QuantStudio 12K Flex
ABI 7900 HT FAST
ABI Veriti Gradient PCR thermocyclers
Agilent 2100 Bioanalyzer
ThermoFisher (Affymetrix) Microarray system
NanoString nCounter MAX System
10XGenomics Chromium Controller

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Publications

Publications associated with this facility (Click To View):

1.) Du Y, Benny PA, Schlueter RJ, Gurary A, Lum-Jones A, Lassiter CB, AlAkwaa FM, Tiirikainen M, Towner D, Ward WS, Garmire LX (2024 Jul 27). Multi-omics Analysis of Umbilical Cord Hematopoietic Stem Cells from a Multi-ethnic Cohort of Hawaii Reveals the Transgenerational Effect of Maternal Pre-Pregnancy Obesity medRxiv, (), 2024.07.27.24310936. . PMCID: 11302719.

2.) Huang BZ, Binder AM, Quon B, Patel YM, Lum-Jones A, Tiirikainen M, Murphy SE, Loo L, Maunakea AK, Haiman CA, Wilkens LR, Koh WP, Cai Q, Aldrich MC, Siegmund KD, Hecht SS, Yuan JM, Blot WJ, Stram DO, Le Marchand L, Park SL (2024 Mar 7). Epigenome-wide association study of total nicotine equivalents in multiethnic current smokers from three prospective cohorts. American journal of human genetics, 111(3), 456-472. . PMID: 38367619.

3.) Kuwabara JT, Hara A, Heckl JR, Peña B, Bhutada S, DeMaris R, Ivey MJ, DeAngelo LP, Liu X, Park J, Jahansooz JR, Mestroni L, McKinsey TA, Apte SS, Tallquist MD (2022 May 13). Regulation of extracellular matrix composition by fibroblasts during perinatal cardiac maturation Journal of molecular and cellular cardiology, 169(), 84-95. . PMCID: 10149041.

4.) Wang Z, Budhu AS, Shen Y, Wong LL, Hernandez BY, Tiirikainen M, Ma X, Irwin ML, Lu L, Zhao H, Lim JK, Taddei T, Mishra L, Pawlish K, Stroup A, Brown R, Nguyen MH, Koshiol J, Hernandez MO, Forgues M, Yang HI, Lee MH, Huang YH, Iwasaki M, Goto A, Suzuki S, Matsuda K, Tanikawa C, Kamatani Y, Mann D, Guarnera M, Shetty K, Thomas CE, Yuan JM, Khor CC, Koh WP, Risch H, Wang XW, Yu H (2021 Dec). Genetic susceptibility to hepatocellular carcinoma in chromosome 22q13.31, findings of a genome-wide association study. JGH open : an open access journal of gastroenterology and hepatology, 5(12), 1363-1372. . PMID: 34950780.

5.) Corley MJ, Sacdalan C, Pang APS, Chomchey N, Ratnaratorn N, Valcour V, Kroon E, Cho KS, Belden AC, Colby D, Robb M, Hsu D, Spudich S, Paul R, Vasan S, Ndhlovu LC (2021 Aug). Abrupt and altered cell-type specific DNA methylation profiles in blood during acute HIV infection persists despite prompt initiation of ART. PLoS pathogens, 17(8), e1009785. doi: 10.1371/journal.ppat.1009785. PMID: 34388205.

6.) Ma C, Hoffmann FW, Marciel MP, Page KE, Williams-Aduja MA, Akana ENL, Gojanovich GS, Gerschenson M, Urschitz J, Moisyadi S, Khadka VS, Rozovsky S, Deng Y, Horgen FD, Hoffmann PR (2021 May). Upregulated ethanolamine phospholipid synthesis via selenoprotein I is required for effective metabolic reprogramming during T cell activation. Molecular metabolism, 47(), 101170. . PMID: 33484950.

7.) Gu Y, Wei X, Sun Y, Gao H, Zheng X, Wong LL, Jin L, Liu N, Hernandez B, Peplowska K, Zhao X, Zhan QM, Feng XH, Tang ZY, Ji J (2018 Dec 7). miR-192-5p silencing by genetic aberrations is a key event in hepatocellular carcinomas with cancer stem cell features Cancer research, 79(5), 941-953. . ID: 6397664.

8.) Ching T, Ha J, Song MA, Tiirikainen M, Molnar J, Berry MJ, Towner D, Garmire LX (2015 Mar 13). Genome-scale hypomethylation in the cord blood DNAs associated with early onset preeclampsia Clinical Epigenetics, 7(1), 21. . ID: 4371797.

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Associations

ABRF

Association of Biomolecular Resource Facilities

Cancer Center

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Metadata

Links

All the links listed resolve to this core profile

https://coremarketplace.org/?FacilityID=787
https://coremarketplace.org/RRID:SCR_019085

Institution

Institution ROR ID: https://ror.org/01wspgy28

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

Keywords:

USEDit, genomic technologies, data analysis, DNA/RNA isolation, plating, and quality analysis, custom genotyping, Real-Time qPCR-based gene expression, copy number and methylation assays, pyrosequencing, ABRF, ABRF

Resource Type:

access service resource, service resource, core facility

Citation:

University of Hawaii at Manoa Cancer Center Genomics and Bioinformatics Shared Resource Core Facility (RRID:SCR_019085)

UHCC Genomics and Bioinformatics Shared Resource (Genomics / Genome Analysis and Technologies)

Quicklinks:

Primary Contact:

Facility RRID

Additional Citation Identifiers

Facility Details

Facility Policies

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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

Cancer Center

(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)

Contact Maarit Tiirikainen

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UHCC Genomics and Bioinformatics Shared Resource

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