# Presentation: 170348

## NHLBI Genomics Core Facility

## New Organizational Structure

**New Organizational Structure**

## 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**

## Resources in the Core

**Resources in the Core**

**Nanodrop spectrophotometer**

**Agilent’s  Lab on a chip**

## GCAS Robot for sample processing 

- GCAS Robot for sample processing

##  Peg Arrays

** ****Peg Arrays**
**Human U133A gene chips only**

**Hyb Oven****	****	****     Fluidic Station****	****	****Scanner**

**Scanner**

## ABI 7900 – Sequence Detection System

**ABI 7900 – Sequence Detection System**
**Q-PCR**

**Perkin Elmer ScanArray 5000XL**

**2 color spotted arrays**

## 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

## Expression Profiling Workflow

- 2 μg

**(Spike in **
**labeling controls)**

**(Spike in **
**hyb controls)**

## Genotyping Workflow

**Restriction Digestion**

- Nsp1

- Nsp1

- Nsp1

**Single Primer Amplification**

**Fragmentation and Labeling**

**Hyb, Wash, and Stain.  Scan and Data Analysis**

**200 – 1100 bases**

- Nsp1

**Day 1**

**Day 2**

**Day 3**

##    Data Flow and Analysis

**Backup **
**servers**

**   ****Scanner**

**NIHLIMS **

**GCOS Client   Signet    Investigator**

** ****DVD archives of data**

**   ****Data Flow and Analysis**

##     Basic Level of Service

**    ****Basic Level of Service**

## Standard Level

**Standard Level**

**Target(s) identification**

**  ****Help with Publication**

## Advanced Analysis

**  ****Collaborate on**
** ****experimental design**

**RNA isolation**

**Amplification of RNA**

**Novel / Complex Statistical Methods**
**(Munson’s group)**

**Novel **
**Pathway Analysis**

**Advanced Analysis**

**co-authorship in publications**
** **

## 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

## Core Policies

**Investigator has to provide chips and samples to the core (We need at least 2****μg 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**

## Contact Information

**Mark Gladwin – 301-435-2310**
**	**_[mgladwin@nhlbi.nih.gov](mailto:mgladwin@nhlbi.nih.gov)_
**Nalini Raghavachari – 301-435-2304**
**	**_[nraghavachari@cc.nih.gov](mailto:mgladwin@nhlbi.nih.gov)_
**Tony Cooper – 301-496-8123**
**	**_[cooperro@mail.nih.gov](mailto:mgladwin@nhlbi.nih.gov)_
**Xiuli Xu 301-402-2102**
**	**_[xux3@nhlbi.nih.gov](mailto:mgladwin@nhlbi.nih.gov)_
**Hangxia Qiu 301-451-6253**
**	****qiuh2@mail.nih.gov**
**Website **
**	****NHLBI/Vascular Medicine Branch/Genomics Core**
**	****contacts, protocols, status of projects, meetings, tutorials **