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All Facilities >> University of Virginia >> UVA Genome Analysis and Technology Core (Genomics / Genome Analysis and Technologies)

UVA Genome Analysis and Technology Core (Genomics / Genome Analysis and Technologies)

Facility Details

About This Facility

Services and Equipment

Publications

Associations

Metadata

University of Virginia

Pinn Hall 1060-1076

1340 Jefferson Park Avenue

Charlottesville, VA 22908

United States of America

https://med.virginia.edu/gatc/

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Quicklinks:

https://coremarketplace.org/med.virginia.edu/gatc/https://coremarketplace.org/RRID:SCR_018883

Facility LIMS Page

https://uva.corefacilities.org/

Primary Contact:

Katia Sol-Church

Last Updated: 08/04/2020

Facility RRID

RRID:SCR_018883

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Facility Grant Number

NCI Cancer Center Support Grant 5P30CA044579

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Facility Details

The mission of the University of Virginia Genome Analysis and Technology Core (GATC) is to serve as a scientific educational resource and biotechnology hub enhancing the scope and quality of basic and translational research. The goal of the core staff is to enable Next Generation Sequencing projects for novice and experienced users, by providing education, and timely assistance in all facets of experimentation from project design and execution to data analysis and reporting. The core champions Scientific Rigor and Reproducibility at all stages of a project life cycle.

Facility Policies

Services are offerred outside of University of Virginia

Consulting is offerred outside of University of Virginia

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Services offered:

10x Genomics

Consultations

Copy Number Variation (CNV)

Customized Protocols

Data Processing And Interpretation

Sequencing - Next Generation Sequencing (NGS)

Single-cell Sequencing

Facility Equipment

[Product Link]

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Illumina NextSeq 500 Sequencing System
10X Genomics Chromium Controller
Illumina MiSeq Sequencing System
Nanopore GridION
Bio-Rad QX200™ Droplet Digital™ PCR System
Applied Biosystems QuantStudio 6 Flex Real Time PCR System
Agilent Bioanalyzer and Tape Station
NanoVue spectrophotometer
Qubit 3.0 fluorometer
Covaris S2
QIAcube
Sage Science Pippin Prep

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Publications

Publications associated with this facility (Click To View):

1.) Pollack KE, Meneveau MO, Melssen MM, Lynch KT, Koeppel AF, Young SJ, Turner S, Kumar P, Sol-Church K, Mauldin IS, Slingluff CL Jr (2020 Apr). Incomplete Freund PMID: 32350119.

2.) Mische SM, Fisher NC, Meyn SM, Sol-Church K, Hegstad-Davies RL, Weis-Garcia F, Adams M, Ashton JM, Delventhal KM, Dragon JA, Holmes L, Jagtap P, Kubow KE, Mason CE, Palmblad M, Searle BC, Turck CW, Knudtson KL (2020 Apr). A Review of the Scientific Rigor, Reproducibility, and Transparency Studies Conducted by the ABRF Research Groups. PMID: 31969795.

3.) Knudtson KL, Carnahan RH, Hegstad-Davies RL, Fisher NC, Hicks B, Lopez PA, Meyn SM, Mische SM, Weis-Garcia F, White LD, Sol-Church K (2019 Sep). Survey on Scientific Shared Resource Rigor and Reproducibility. PMID: 31452645.

4.) Operario DJ, Pholwat S, Koeppel AF, Prorock A, Bao Y, Sol-Church K, Scheurenbrand M, Poulter M, Turner S, Parikh HI, Mathers A, Houpt ER (2019 Aug 1). Mycobacterium avium Complex Diversity within Lung Disease, as Revealed by Whole-Genome Sequencing. PMID: 30965019.

5.) LaCroix AJ, Stabley D, Sahraoui R, Adam MP, Mehaffey M, Kernan K, Myers CT, Fagerstrom C, Anadiotis G, Akkari YM, Robbins KM, Gripp KW, Baratela WAR, Bober MB, Duker AL, Doherty D, Dempsey JC, Miller DG, Kircher M, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics., Mefford HC, Sol-Church K (2019 Jan 3). GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome. PMID: 30554721.

6.) Stabley DL, Holbrook J, Harris AW, Swoboda KJ, Crawford TO, Sol-Church K, Butchbach MER (2017 May). Establishing a reference dataset for the authentication of spinal muscular atrophy cell lines using STR profiling and digital PCR. PMID: 28284873.

7.) Wang Y, Li J, Kolon TF, Olivant Fisher A, Figueroa TE, BaniHani AH, Hagerty JA, Gonzalez R, Noh PH, Chiavacci RM, Harden KR, Abrams DJ, Stabley D, Kim CE, Sol-Church K, Hakonarson H, Devoto M, Barthold JS (2016 Oct 21). Genomic copy number variation association study in Caucasian patients with nonsyndromic cryptorchidism. PMID: 27769252.

8.) Stabley DL, Harris AW, Holbrook J, Chubbs NJ, Lozo KW, Crawford TO, Swoboda KJ, Funanage VL, Wang W, Mackenzie W, Scavina M, Sol-Church K, Butchbach ME (2015 Jul). SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR. PMID: 26247043.

9.) Kolb EA, Sampson V, Stabley D, Walter A, Sol-Church K, Cripe T, Hingorani P, Ahern CH, Weigel BJ, Zwiebel J, Blaney SM (2015 May). A phase I trial and viral clearance study of reovirus (Reolysin) in children with relapsed or refractory extra-cranial solid tumors: a Children PMID: 25728527.

10.) Logan JG, Yun S, Bao Y, Farber E, Farber CR (2020 May 6). RNA-sequencing analysis of differential gene expression associated with arterial stiffness. PMID: 32375599.

11.) Nicolau CA, Prorock A, Bao Y, Neves-Ferreira AGDC, Valente RH, Fox JW (2018 Feb 6). Revisiting the Therapeutic Potential of Bothrops jararaca Venom: Screening for Novel Activities Using Connectivity Mapping. PMID: 29415440.

12.) Operario DJ, Koeppel AF, Turner SD, Bao Y, Pholwat S, Banu S, Foongladda S, Mpagama S, Gratz J, Ogarkov O, Zhadova S, Heysell SK, Houpt ER (2017). Correction: Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis. PMID: 28686689.

13.) Operario DJ, Koeppel AF, Turner SD, Bao Y, Pholwat S, Banu S, Foongladda S, Mpagama S, Gratz J, Ogarkov O, Zhadova S, Heysell SK, Houpt ER (2017). Prevalence and extent of heteroresistance by next generation sequencing of multidrug-resistant tuberculosis. PMID: 28545050.

14.) Mauldin IS, Wang E, Deacon DH, Olson WC, Bao Y, Slingluff CL Jr (2015 Sep 15). TLR2/6 agonists and interferon-gamma induce human melanoma cells to produce CXCL10. PMID: 25765738.

15.) Aramadhaka LR, Prorock A, Dragulev B, Bao Y, Fox JW (2013 Jul). Connectivity maps for biosimilar drug discovery in venoms: the case of Gila monster venom and the anti-diabetes drug Byetta®. PMID: 23602926.

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Associations

Cancer Center

ABRF

Association of Biomolecular Resource Facilities

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Metadata

Links

All the links listed resolve to this core listing

https://coremarketplace.org/?FacilityID=1024
https://coremarketplace.org/med.virginia.edu/gatc/
https://coremarketplace.org/RRID:SCR_018883

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

Keywords:

USEDit, genome analysis, NGS genomic, transcriptomics, RNA Seq, CHIP Seq, ATAC Seq, Amplicon DNA Seq, 16S ribosomal gene sequencing, shot gun sequencing

Resource Type:

Resource, service resource, core facility, access service resource

Citation:

Virginia University School of Medicine Genome Analysis and Technology Core Facility (RRID:SCR_018883)

UVA Genome Analysis and Technology Core (Genomics / Genome Analysis and Technologies)

Quicklinks:

Facility LIMS Page

Primary Contact:

Facility RRID

Facility Grant Number

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

Cancer Center

ABRF

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

Metadata

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

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