Department of Genetics

Genomics Core

Mission

The Genomics Core serves the Einstein scientific community by providing a broad scala of services, utilizing current and emerging nucleic acid technologies. Microarrays, real-time PCR, Sanger sequencing and new, massively parallel sequencing (MPS; also known as next-gen sequencing) are available. The Core provides a number of technologies for genotyping DNA from humans or model organisms, varying from SNP (single nucleotide polymorphism) detecting to sequencing DNA for unknown variations. Furthermore, the Genomics Core performs quantitative CpG methylation analysis for the Epigenomics Core.

Services

DNA Sequencing & Genotyping Technologies

  • Traditional DNA sequencing (ABI 3730)- tubes for single samples or 96 well plates
    • Optional PCR or plasmid purification prior to sequencing
  • MPS (Next Gen Sequencing)- Massively Parallel Sequencing
    • Illumina GAII—36+ bp reads; useful for large genomes
    • Roche 454—400+ bp reads; useful for de novo sequencing and microorganisms
  • Sequenom EpiTyper - for Quantitative Cytosine Methylation
  • Sequenom iPLEX - multiplex SNP genotyping by Single Base Extension; 1-40 SNPs/assay
  • Pyrosequencing – singleplex typing of SNPs with sequence context.
  • Fragment analysis - microsatellite markers; Multiplex Ligation-dependent Probe Amplification (MLPA) for detection of copy number and genomic disorders.

Microarry & Expression Technologies

  • Microarrays
    • Affymetrix Exon Arrays for gene expression and splice variant analysis
      • Gene 1.0 ST – new, lower cost arrays for gene expression
      • SNP 6.0 arrays: Genome-wide SNP and copy number variant typing- 1.8 M markers
    • NimbleGen – ChIP on Chip, HELP-Chip
  • Real Time qPCR (ABI 7900) 384 well and 96 well instruments
    • Quantitative gene expression,
    • HRM (High Resolution Melting) – SNP discovery
    • Copy number analysis
  • Sequenom QGE – multiplex quantitative gene expression and copy number analysis
  • Bioanalyzer - RNA and DNA Quality Analysis with Agilent Bioanalyzer 2100
    • Nanodrop – RNA and DNA quantitation

SAMPLE SUBMISSION
Orders for all services may be placed through the Core’s Laboratory Information Management System, GeneSifter. Researchers and PIs enter sample information to track the status of their samples and receive data. To ease the entry of large numbers of sample names and information in the order forms look for the excel icon. Press this to download an excel table formatted for your current GeneSifter form. Fill it out with excel, then go back to the GeneSifter form and upload the file with the upload icon.

DATA ANALYSIS
Data is made available to researchers and their PIs through the Core’s Laboratory Information Management System, GeneSifter. The data is screened with appropriate quality control measures. The Genomics Core provides file formats that are ready for analysis. Assistance with retrieving data, instructions as to how to use the tools and more extensive data analysis on a fee-for-service basis are provided by the Computational Genomics Core (Link to the Computational Genomics Core).

Analytical resources are available to AECOM researchers at the Analytical Tools website maintained by the Computational Genomics Core. This site includes CLC Genomics Workbench, Ingenuity Pathway Analysis, R/BioConductor and more. Additional resources for microarray analyses are available at GenePattern.

Location

Price Center Room 413.
Deposit DNA samples in the undercounter refrigerator. Deposit RNA samples in the undercounter freezer. Both are marked “Sample Deposit.”
Samples for Traditional Sequencing may be dropped off in these additional locations:
Ullmann Building, Room 713 – Sample Refrigerator

After Hours, Weekends and Holidays:
The Price Center, Room 405– Cold Room Dropbox
Ullmann Building, Room 718 – Cold Room Dropbox
New Dropbox locations will be announced.

Personnel

Faculty Advisor
Bernice Morrow, Ph.D.
718.678.1121
morrow@einstein.yu.edu 

Director
David Reynolds
718.678.1157
dreynold@einstein.yu.edu 

Staff
Elsa Boschen
Wen Tran
Christina Lowes
Limin Wang
Kevin Lau 

Phone: 718.678.1160
Fax: 718.678.1016

Selected Publications

Leukemia, 2006 Apr;20(4):556-62
Endocrinology, 2006 Jul;147(7):3375-90
Immunity, 2006 Apr;24(4):393-403

 

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