NHLBI Genomics Core Facility

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NHLBI Genomics Core Facility
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New Organizational Structure
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Primary Goals

• To provide investigators with high quality,
  state-of-the-art gene expression profiling
  genotyping services in a timely fashion using the
  affymetrix platform
• rigorous standardization of protocols and
  multiple quality control checks
• To provide streamlined data analysis and identify
  signature genes
• Application of complex statistical tools

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Resources in the Core
Nanodrop spectrophotometer
Agilents Lab on a chip
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GCAS Robot for sample processing
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Hyb Oven Fluidic Station Scanner
Peg Arrays Human U133A gene chips only
Scanner
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ABI 7900 Sequence Detection System Q-PCR
Perkin Elmer ScanArray 5000XL
2 color spotted arrays
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Application software in the core

• GCOS - Data collection
• MSCL Toolbox - Normalization/Analysis
• Jmp - Data Set Analysis
• Genespring - Data Set Analysis
• Partek Pro - Normalization/Analysis
• Ingenuity - Pathway analysis
• Metacore - Pathway Analysis

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Expression Profiling Workflow
(Spike in labeling controls)
2 µg
(Spike in hyb controls)
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Genotyping Workflow
250 ng Genomic DNA
Restriction Digestion
Day 1
Nsp1
Nsp1
Nsp1
Nsp1
200 1100 bases
Single Primer Amplification
Day 2
Hyb, Wash, and Stain. Scan and Data Analysis
Day 3
Fragmentation and Labeling
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Data Flow and Analysis
Scanner
GCOS Client Signet Investigator
NIHLIMS
Backup servers
DVD archives of data
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Basic Level of Service

• Online access to project data

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Standard Level
Help with Publication
Target(s) identification
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Advanced Analysis
Collaborate on experimental design
co-authorship in publications
RNA isolation
Amplification of RNA
Novel / Complex Statistical Methods (Munsons
group)
Novel Pathway Analysis
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New Service Initiatives

• Taqman Low Density Arrays (can analyze 8 samples
  for 24 different genes)
• Exon and Tiling Array Mapping
• Method development for the isolation and analysis
  of picogram amounts of RNA in collaboration with
  bio-tech companies
• Service for non NHLBI investigators at a nominal
  cost

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Core Policies

• Investigator has to provide chips and samples to
  the core (We need at least 2µg total RNA in 4µl
  volume, 250ng genomic DNA)
• Submitted RNA/DNA samples should be of good
  quality
• Description of project / sample information
• It is advisable to have an n of 5-6 for each
  group to have a good statistical power for
  analysis
• If you have only one or 2 samples per group, the
  core wont be responsible for data quality
• Turn around time is 2 weeks since the receipt of
  samples
• You will be notified by email the status of your
  project and upon completion will send you QC
  data
• If a problem arises with the analysis of one or
  more of your specimens, you will be contacted
  immediately

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Contact Information

• Mark Gladwin 301-435-2310
• mgladwin_at_nhlbi.nih.gov
• Nalini Raghavachari 301-435-2304
• nraghavachari_at_cc.nih.gov
• Tony Cooper 301-496-8123
• cooperro_at_mail.nih.gov
• Xiuli Xu 301-402-2102
• xux3_at_nhlbi.nih.gov
• Hangxia Qiu 301-451-6253
• qiuh2_at_mail.nih.gov
• Website
• NHLBI/Vascular Medicine Branch/Genomics Core
• contacts, protocols, status of projects,
  meetings, tutorials