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The Scripps Research Institute NGS and Microarray Core

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La Jolla, California, US

About The Scripps Research Institute NGS and Microarray Core

The TSRI DNA Array Core Facility was established in 1998 to provide microarray technology to the Scripps research community. Since then the scope has been expanded to include a variety of related services and resources, for example: Sample Quantification, Genotyping, Gene Expression Analysis, and a Data... Show more »

The TSRI DNA Array Core Facility was established in 1998 to provide microarray technology to the Scripps research community. Since then the scope has been expanded to include a variety of related services and resources, for example: Sample Quantification, Genotyping, Gene Expression Analysis, and a Data Analysis and Statistics Resource. In addition the DNA Array Core provides custom spotted arrays, image analysis, and general statistics consulting. The DNA ARRAY Core is an active participant in several research projects at TSRI: The Consortium for Functional Glycomics, General Clinical Research Center (GCRC), The Scripps NeuroAIDS Preclinical Studies (SNAPS) Center, Transplant Genomics Collaborative Group Program Project, and the Vision Research Core Center.

Recent Publications:

Kurian SM, Williams AN, Gelbart T, Campbell D, Mondala TS, Head SR, Horvath S, Gaber L, Thompson R, Whisenant T, Lin W, Langfelder P, Robison EH, Schaffer RL, Fisher JS, Friedewald J, Flechner SM, Chan LK, Wiseman AC, Shidban H, Mendez R, Heilman R, Abecassis MM, Marsh CL, Salomon DR. (2014) Molecular classifiers for acute kidney transplant rejection in peripheral blood by whole genome gene expression profiling. Am J Transplant. May;14(5):1164-72. doi: 10.1111/ajt.12671. Epub 2014 Apr 11.

Zilio N, Codlin S, Vashisht AA, Bitton DA, Head SR, Wohlschlegel JA, Bähler J, Boddy MN (2014) A novel histone deacetylase complex in the control of transcription and genome stability. Mol Cell Biol. Sep 15;34(18):3500-14. doi: 10.1128/MCB.00519-14. Epub 2014 Jul 7.

Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ, Head SR, Duester G, Si Dong PD, Rana TM. (2014) An Evolutionarily Conserved Long Noncoding RNA TUNA Controls Pluripotency and Neural Lineage Commitment. Mol Cell. 2014 Feb 11. pii: S1097-2765(14)00082-3. doi: 10.1016/j.molcel.2014.01.021

Head SR, Komori HK, Lamere SA, Whisenant T, Van Nieuwerburgh F, Salomon DR, Ordoukhanian P (2014). Library construction for next-generation sequencing: Overviews and challenges. Biotechniques. Feb 1;56(2):61-77.

Ruwona TB, McBride R, Chappel R, Head SR, Ordoukhanian P, Burton DR, Law M. Optimization of peptide arrays for studying antibodies to hepatitis C virus continuous epitopes (2014). J Immunol Methods. Jan 15;402(1-2):35-42.

Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S (2014). Technical Variations in Low-Input RNA-seq Methodologies. Sci Rep. Jan 14;4:3678.

Li Z, Chao TC, Chang KY, Lin N, Patil VS, Shimizu C, Head SR, Burns JC, Rana TM (2014). The long noncoding RNA THRIL regulates TNF? expression through its interaction with hnRNPL. Proc Natl Acad Sci U S A. Jan 21;111(3):1002-7.

Krishnaswami SR, Kumar S, Ordoukhanian P, Yu BD (2014) Fate and Plasticity of the Epidermis in Response to Congenital Activation of BRAF. J Invest Dermatol. 2014 Sep 9. doi: 10.1038/jid.2014.388. [Epub ahead of print] PMID: 25202828

Helsmoortel C, Vandeweyer G, Ordoukhanian P, Van Nieuwerburgh F, Van der Aa N, Kooy RF. Challenges and opportunities in the investigation of unexplained intellectual disability using family based whole exome sequencing. Clin Genet. (2014) doi: 10.1111/cge.12470. PMID: 25081361

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Our Services (15)


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Multiplex PCR

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Fluidigm Biomark HD

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Illumina NGS Library Preparation

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The Scripps Research Next Generation Sequencing Core Facility housed in 250 MEM was established in 2008. Instruments that are currently active in the core include: Illumina Miseq and HiSeq; Ion Torrent Proton and PGM; and a Fluidigm Biomark HD.

The Scripps Research Next Generation Sequencing Core Facility housed in 250 MEM was established in 2008. Instruments that are currently active in the core include: Illumina Miseq and HiSeq; Ion Torrent Proton and PGM; and a Fluidigm Biomark HD.

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Custom Microarrays

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The Microarray Core Facility has instrumentation and experience in spotted microarray manufacture, hybridization, confocal scanning and data analysis. Custom spotted microarrays can be printed with a variety of materials including glycans, carbohydrates, peptides, glycopeptides, small molecules, DNA/RNA, proteins and any other... Show more »

The Microarray Core Facility has instrumentation and experience in spotted microarray manufacture, hybridization, confocal scanning and data analysis. Custom spotted microarrays can be printed with a variety of materials including glycans, carbohydrates, peptides, glycopeptides, small molecules, DNA/RNA, proteins and any other client provided reagents.

Since 2005 we have manufactured and provided the Mammalian Glycan Array for the Consortium for Functional Glycomics (CFG) which is available as a fee-for-service screening tool at Emory University (CFG Mammalian Glycan Array Service). As of November 2014, a Microbial Glycan Microarray (MGM) comprised of glycans sourced from multiple bacterial species will be available via the same fee-for-service mechanism. More information about the composition of the array and the bacterial species represented can be found here.

In addition to in-house manufactured arrays, we will assist with other custom or commercial arrays which are compatible with confocal micrarray scanners (e.g. Agilent, ProtoArray, LecChip).

Our lab is equipped with a wide variety of instruments, which in combination provide our customers with a state-of-the-art custom printing facility. Our services include: Preparation of your samples, production of custom arrays, and processing, scanning and analysis of your arrayed slides. Our customers are directly involved with the design of their arrays. In addition, our customers are trained on all protocols and procedures involved for custom arraying and slide processing.

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LecChip ProtoArray

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Microarray Data Analysis

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Gene expression, SNP Genotyping and Cytogenetics

Affymetrix GeneChip Arrays

Affymetrix GeneChips remain a principle tool for high throughput gene expression analysis. The Microarray Core offers Affymetrix array analysis using both cartridge array and high throughput GeneTitan (16, 24, and 96 array plate). Assays include gene expression, genotyping and cytogenetics.

Gene expression, SNP Genotyping and Cytogenetics

Affymetrix GeneChip Arrays

Affymetrix GeneChips remain a principle tool for high throughput gene expression analysis. The Microarray Core offers Affymetrix array analysis using both cartridge array and high throughput GeneTitan (16, 24, and 96 array plate). Assays include gene expression, genotyping and cytogenetics.

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DNA Library Preparation

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Next Generation Sequencing (NGS)

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Biochemistry & Molecular Biology

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DNA Microarrays

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Nucleic Acid Services

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Biology

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PCR

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PCR Services

PCR Services

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Nucleic Acid Data Analysis

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DNA Services

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DNA Sequencing

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Nucleic Acid Analysis

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Steven Head

Co-Director, Next Generation Sequencing

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