The Genomics Core Laboratory (GCL) is the Microarray Core Facility of MSKCC. Since its inception in January 2001, we have processed more than 6,000 samples. Our specialty is the processing of very small samples for the Affymetrix array (laser capture microdissected tissues or cells, fine needle aspiration samples, core biopsies, FAC-sorted cells).

We are a full-service facility, from experimental design and RNA extraction to data analysis and validation of your array data by Q-PCR. The services we provide can be separated into two categories:

1. RNA analysis ( extraction, microarray, and Q-PCR).
2. DNA analysis (DNA extraction, CGH, CpG and SNP array, Q-PCR).

We offer commercial microarray platform: Affymetrix GeneChip^® array and Agilent array. We also have in-house spotted array (cDNA, Oligo, BAC CGH array, and CpG island array).

Services

RNA Analysis

• RNA extraction.
  - from tissue
  - from cell
  - from blood
• RNA quality control and quantification.
  - on Agilent Bioanalyzer
  - with Nanodrop
• cDNA synthesis.
  - for Quantitative-PCR
  - for other purposes
• Microarray.
  - experimental design
  - Affymetrix GeneChip^® array
  - in-house spotted array (Oligo and cDNA) for human and mouse
  - data analysis (see below)
• Real-time PCR.
  - on Biorad Icycler

DNA Analysis

• DNA extraction.
  - from tissue
  - from cell
  - from blood
• SNP analysis.
  - Affymetrix Human Mapping 100K system
• Chromosomal abnormality -- CGH BAC array.
  - for mouse (1MB resolution clone set)
  - for human (1 MB resolution clone set)

Microarray Data Analysis

• Weekly training for new users.
  - for GeneChip^® Operating Software (formerly MicroArray Suite)
  - for NetAffx™ (Functional annotation of data)
  - for in-house analytical tools
• Monthly training.
  - for GeneSpring
• Tutorial.
  - introduction to microarray tools and analysis
  - microarray analysis in Excel software

Visit the Tri-Institutional Web site: www.triiprograms.org for more information.