Next Generation Sequencing Core

We encourage parties interested in using our facility to set up a meeting with Steven Head or Phil Ordoukhanian to discuss details and specifics about experimental design, sample preparation and costs. Our facility has extensive experience in preparation of sequencing libraries as well as novel sequencing technology applications.

Phone: (858) 784-2263
Steven Head
Phil Ordoukhanian

Ctr. Protein/Nucleic Acid Core
Microarray Core

The Scripps Research Next Generation Sequencing (NGS) Core is a full-service facility providing library preparation and sequencing services. The facility currently operates Illumina and Ion Torrent sequencing systems, as well as a Fluidigm, Biomark HD, high throughput real-time PCR and digital PCR system.

Our Illumina Hiseq2000 system typically generates 100 base single-end reads or 2 X 100 paired ends reads with outputs up to 200 milion reads per lane and 8 lanes per flowcell. The Illumina Miseq sequencing system is used for 2 X 75 base or 2 X 300 base reads, generating up to 25 million reads per run.

The Ion Torrent sequencing systems include, the Proton, currently generating 80 million reads on the PI chip (read lengths averaging 150 bases), and the PGM averaging read lengths around 400 bases up to 5 million reads per run.

The BioMark™ HD System performs high throughput real-time PCR and digital PCR, integrating thermal cycling and fluorescence detection. 96 samples can be tested with 96 PCR primer sets generating 9,216 qPCR data points in a single run. Protocols for single-cell qPCR have been successfully implemented on our system. Using the Fluidigm Access Array, one can PCR amplify 48 different samples with up to 48 different PCR primer sets and recover the products for Next Generation Sequencing analysis.

Fluidigm Biomark HD

Our Fluidigm BioMark™ HD System is housed in the 3040 Science Park lab (Room 290). This instrument is currently operated as an open access system. A user fee will be assessed based on usage to recover costs associated with the yearly service contract. Users should contact Steve Head by email or at (858) 784-2263.

PCR Primer sets for Genotyping, Gene Expression and Targeted Resequencing can be ordered from Fluidigm.

Data Analysis

Sample Submittal

To submit samples, please contact Steve Head by email or at (858) 784-2263.

If sending samples by mail, send to:

Attn: John Shimashita, MEM250
9365 Waples St., Suite E
San Diego, CA 92121

Drop-off location:
Medical and Experimental Medicine Building (MEM)
3545 Cray Court, Rm 250/256
San Diego, CA 92121
  • Kurian SM, Williams AN, Gelbart TCampbell DMondala TSHead 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 RChappel RHead SROrdoukhanian 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 SROrdoukhanianP, 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
  • Dosanjh A, Robison EMondala THead SR, Salomon DR, Kurian SM, (2013). Genomic meta-analysis of growth factor and integrin pathways in chronic kidney transplant injury. BMC Genomics. Apr 23;14:275. doi: 10.1186/1471-2164-14-275.
  • Verma-Gaur J, Torkamani A, Schaffer LHead SR, Schork NJ, Feeney AJ (2012). Noncoding transcription within the Igh distal V(H) region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells. Proc Natl Acad Sci U S A. Oct 16;109(42):17004-9.
  • Routh A, Ordoukhanian P, Johnson JE (2012). Nucleotide-resolution profiling of RNA recombination in the encapsidated genome of a eukaryotic RNA virus by next-generation sequencing. J Mol Biol 424, 257-69. PMC 3502730
  • Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian PHead SR. (2012) Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Res. Feb 1;40(3):e24. Epub 2011 Nov 29.
  • Van Nieuwerburgh F, Soetaert S, Podshivalova K, Ay-Lin Wang E, Schaffer L, Deforce D, Salomon DR, Head SR, Ordoukhanian P(2011). Quantitative bias in Illumina TruSeq and a novel post amplification barcoding strategy for multiplexed DNA and small RNA deep sequencing. PLoS One.;6(10):e26969. Epub 2011 Oct 28.
  • Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell DHead SR, Yates JR 3rd, Salomon DR. (2011). MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes. J Immunol. Sep 1;187(5):2233-43. Epub Jul 25.
  • Chang LM, Maheshwari P, Werth S, Schaffer LHead SR, Kovarik C, Werth VP (2011).Identification and molecular analysis of glycosaminoglycans in cutaneous lupus erythematosus and dermatomyositis. J Histochem Cytochem. Mar;59(3):336-45. Epub 2011 Jan 12.
  • Head SR, Komori HK, Hart GT, Shimashita J, Schaffer L, Salomon DR, Ordoukhanian PT(2011). Method for improved Illumina sequencing library preparation using NuGEN Ovation RNA-Seq System. Biotechniques. Mar;50(3):177-80.
  • Flaherty BL, Van Nieuwerburgh F, Head SR, Golden JW (2011). Directional RNA deep sequencing sheds new light on the transcriptional response of Anabaena sp. strain PCC 7120 to combined-nitrogen deprivation. BMC Genomics. Jun 28;12:332. PMC3141674
  • Komori HK, Lamere SA, Torkamani A, Hart GT, Kotsopoulos S, Warner J, Samuels ML, Olson J, Head SROrdoukhanian P, Lee PL, Link DR, Salomon DR (2011). Application of microdroplet PCR for large-scale targeted bisulfite sequencing. Genome Res. Aug 25. [Epub ahead of print].
  • Grigoryev YA, Kurian SM, Hart T, Nakorchevsky AA, Chen C, Campbell DHead SR, Yates JR 3rd, Salomon DR. (2011). MicroRNA Regulation of Molecular Networks Mapped by Global MicroRNA, mRNA, and Protein Expression in Activated T Lymphocytes. J Immunol. Sep 1;187(5):2233-43. Epub Jul 25.
  • Tang B, Di Lena P, Schaffer LHead SR, Baldi P, Thomas EA  (2011). Genome-wide identification of bcl11b gene targets reveals role in brain-derived neurotrophic factor signaling. PLoS One. 2011;6(9):e23691. Epub Sep 1.
  • Grigoryev YA, Kurian SM, Avnur Z, Borie D, Deng J, Campbell D, Sung J, Nikolcheva T, Quinn A, Schulman H, Peng SL, Schaffer R, Fisher J, Mondala THead S, Flechner SM, Kantor AB, Marsh C, Salomon DR (2010). Deconvoluting post-transplant immunity: cell subset-specific mapping reveals pathways for activation and expansion of memory T, monocytes and B cells. PLoS One. Oct 14;5(10):e13358.
  • Rozenzhak S, Mejía-Ramírez E, Williams JS, Schaffer L, Hammond JAHead SR, Russell P (2010). Rad3 decorates critical chromosomal domains with gammaH2A to protect genome integrity during S-Phase in fission yeast. PLoS Genet. Jul 22;6(7):e1001032. 
  • Greenbaum JA, Assarsson E, Chung JL, Head S, Sette A, Peters B (2010). TiArA: a virtual appliance for the analysis of Tiling Array data. PLoS One. Apr 1;5(4):e9993.
  • Nakorchevsky A, Hewel JA, Kurian SM, Mondala TSCampbell DHead SR, Marsh CL, Yates JR 3rd, Salomon DR (2010). Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies. J Am Soc Nephrol. Feb;21(2):362-73. Epub Jan 2
  • Moutaftsi M, Tscharke DC, Vaughan K, Koelle DM, Stern L, Calvo-Calle M, Ennis F, Terajima M, Sutter G, Crotty S, Drexler I, Franchini G, Yewdell JW, Head SR, Blum J, Peters B, Sette A (2010). Uncovering the interplay between CD8, CD4 and antibody responses to complex pathogens. Future Microbiol. Feb;5(2):221-39.
  • Robison EHMondala TS, Williams AR, Head SR, Salomon DR, Kurian SM (2009). Whole genome transcript profiling from fingerstick blood samples: a comparison and feasibility study. BMC Genomics. Dec 17;10:617.
  • Grigoryev YA, Kurian SM, Nakorchevskiy AA, Burke JP, Campbell DHead SR, Deng J, Kantor AB, Yates JR 3rd, Salomon DR. (2009 ). Genome-wide analysis of immune activation in human T and B cells reveals distinct classes of alternatively spliced genes. PLoS One. Nov 19;4(11):e7906.
  • Montpetit ML, Stocker PJ, Schwetz TA, Harper JM, Norring SA, Schaffer L, North SJ, Jang-Lee J, Gilmartin T, Head SR, Haslam SM, Dell A, Marth JD, Bennett ES, (2009). Regulated and aberrant glycosylation modulate cardiac electrical signaling. Proc Natl Acad Sci U S A. Aug 7. [Epub ahead of print]
  • Kurian SM, Heilman R, Mondala TS, Nakorchevsky A, Hewel JA, Campbell DRobison EH, Wang L, Lin W, Gaber L, Solez K, Shidban H, Mendez R, Schaffer RL, Fisher JS, Flechner SM, Head SR, Horvath S, Yates JR, Marsh CL, Salomon DR. (2009). Biomarkers for early and late stage chronic allograft nephropathy by proteogenomic profiling of peripheral blood. PLoS One. Jul 10;4(7):e6212.
  • Pebernard S, Schaffer L, Campbell DHead SR, Boddy MN (2008). Localization of Smc5/6 to centromeres and telomeres requires heterochromatin and SUMO, respectively. EMBO J. 2008 Nov 19;27(22):3011-23. Epub 2008 Oct 16.
  • Xu CR, Schaffer LHead SR, Feeney AJ. (2008) Reciprocal patterns of methylation of H3K36 and H3K27 on proximal vs. distal IgVH genes are modulated by IL-7 and Pax5. Proc Natl Acad Sci U S A. Jun 24;105(25):8685-90. Epub 2008 Jun 17.
  • Marcos NT, Magalhães A, Ferreira B, Oliveira MJ, Carvalho AS, Mendes N, Gilmartin THead SR, Figueiredo C, David L, Santos-Silva F, Reis CA. (2008) Helicobacter pylori induces beta3GnT5 in human gastric cell lines, modulating expression of the SabA ligand sialyl-Lewis x. J Clin Invest. Jun;118(6):2325-36. 
  • Benhnia MR, McCausland MM, Su HP, Singh K, Hoffmann J, Davies DH, Felgner PL, Head S, Sette A, Garboczi DN, Crotty S (2008). Redundancy and plasticity of neutralizing antibody responses are cornerstone attributes of the human immune response to the smallpox vaccine. J Virol. Apr;82(7):3751-68.
  • Assarsson E, Greenbaum JA, Sundström M, Schaffer LHammond JA, Pasquetto V, Oseroff C, Hendrickson RC, Lefkowitz EJ, Tscharke DC, Sidney J, Grey HM, Head SR, Peters B, Sette A. (2008). Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes. Proc Natl Acad Sci U S A. Feb 12;105(6):2140-5.
  • Bax M, García-Vallejo JJ, Jang-Lee J, North SJ,Gilmartin TJ, Hernández G, Crocker PR, Leffler H, Head SR, Haslam SM, Dell A, van Kooyk Y (2007). Dendritic cell maturation results in pronounced changes in glycan expression affecting recognition by siglecs and galectins. J Immunol. Dec 15;179 (12):8216-24.
  • Desplats PA, Denny CA, Kass KE, Gilmartin THead SR, Sutcliffe JG, Seyfried TN, Thomas EA. (2007) Glycolipid and ganglioside metabolism imbalances in Huntington's disease. Neurobiol Dis. Sep;27 (3): 265-77
  • Kurian S, Grigoryev Y, Head SCampbell DMondala T, Salomon DR. (2007) Applying genomics to organ transplantation medicine in both discovery and validation of biomarkers. Int Immunopharmacol. Dec 20;7(14):1948-60.
  • Sampathkumar SG, Jones MB, Meledeo MA, Campbell CT, Choi SS, Hida K, Gomutputra P, Sheh A, Gilmartin THead SR, Yarema KJ (2006). Targeting glycosylation pathways and the cell cycle: sugar-dependent activity of butyrate-carbohydrate cancer prodrugs. Chem Biol. Dec;13(12):1265-75.
  • Hammond JAHead SR(2006). Expression profiling of glycosyltransferases and related enzymes using gene microarrays. Methods Enzymol.416:141-56.
  • Cirz RT, O'neill BM, Hammond JAHead SR, Romesberg FE. (2006). Defining the Pseudomonas aeruginosa SOS Response and Its Role in the Global Response to the Antibiotic Ciprofloxacin. J Bacteriol. Oct;188(20):7101-10. 
  • Liang FS, Greenberg WA, Hammond JAHoffmann JHead SR, Wong CH (2006). Evaluation of RNA-binding specificity of aminoglycosides with DNA microarrays. Proc Natl Acad Sci U S A. Aug 15;103(33):12311-6.
  • Comelli EM, Sutton-Smith M, Yan Q, Amado M, Panico M, Gilmartin TWhisenant TLanigan CM, Head SR, Goldberg D, Morris H, Dell A, and James Paulson JC (2006). Activation of CD4+ and CD8+ T Lymphocytes Leads to Dramatic Remodeling of N-linked Glycans. Aug 15;177(4):2431-40 The Journal of Immunology.
  • Huang CY, Thayer DA, Chang AY, Best MD, Hoffmann JHead S, Wong CH. (2006). Carbohydrate microarray for profiling the antibodies interacting with Globo H tumor antigen. Proc Natl Acad Sci U S A. Jan 3;103(1):15-20. Epub 2005 Dec 22.
  • Desplats PA, Kass KE, Gilmartin T, Stanwood GD, Woodward EL, Head SR, Sutcliffe JG, Thomas EA. (2006). Selective deficits in the expression of striatal-enriched mRNAs in Huntington's disease. J Neurochem. Feb;96(3):743-57
  • Kurian SM, Flechner SM, Kaouk J, Modlin C, Goldfarb D, Cook DJ, Head S, Salomon DR (2005). Laparoscopic donor nephrectomy gene expression profiling reveals upregulation of stress and ischemia associated genes compared to control kidneys. Transplantation. Oct 27;80(8):1067-71.
  • Blixt O, Head SMondala T, Scanlan C, Huflejt ME, Alvarez R, Bryan MC, Fazio F, Calarese D, Stevens J, Razi N, Stevens DJ, Skehel JJ, van Die I, Burton DR, Wilson IA, Cummings R, Bovin N, Wong C-H and Paulson JC (2004). Printed covalent glycan array for ligand profiling of diverse glycan binding proteins. Proc Natl Acad Sci U S A. Dec 7;101(49):17033-8.
  • Sieber SA, Mondala TSHead SR, Cravatt BF (2004). A microarray platform for profiling enzyme activities in complex proteomes. J Am Chem Soc. Dec 8;126(48):15640-1.
  • Flechner SM, Kurian SM, Solez K, Cook DJ, Burke JT, Rollin H, Hammond JAWhisenant TLanigan CMHead SR, Salomon DR (2004). De novo kidney transplantation without use of calcineurin inhibitors preserves renal structure and function at two years. Am J Transplant. Nov;4(11):1776-85.
  • Kunicki TJ, Federici AB, Salomon DR, Koziol JA, Head SRMondala TSChismar JD, Baronciani L, Canciani MT, Peake IR. (2004). An association of candidate gene haplotypes and bleeding severity in Von Willebrand Disease (VWD) type 1 pedigrees. Blood. Oct 15;104(8):2359-67.
  • Flechner SM, Kurian SM, Head SR, Sharp SM, Whisenant TC, Zhang J, Horvath S, Mondala TGilmartin T, Cook DJ, Kay SA, Walker, JR, and Salomon DR (2004). Characterizing Acute Kidney Transplant Rejection by Gene Profiling of Biopsies and Peripheral Blood Lymphocytes. Am J Transplant. 2004 Sep;4(9):1475-89.
  • Chismar, JMondala, T, Fox, H, Roberts, E,  Langford, D,  Masliah, E, Salomon, DR ,and Head, SR. (2002) Analysis of result variability from high-density Affymetrix oligonucleotide arrays comparing same-species (human/human) and cross-species (human/monkey) hybridizations. Biotechniques.Sep;33(3):516-524.
  • Head SR, Parikh K, Rogers Y, Bishai W, Goelet P, Boyce-Jacino MT (1999).  Solid-phase sequence scanning for drug resistance detection in tuberculosis. Mol Cell Probes 13(2):81-87.
  • Head SR, Rogers Y-H, Parikh K, Lan G, Anderson S, Goelet P, & Boyce-Jacino, MT, (1997).  Nested Genetic Bit Analysis (N-GBA) for mutation detection in the human p53 gene.  Nucleic Acids Res 25 (24): 5065-5071