# Presentation: 264501

## Slide 1

## Expression Assay Process Flow

**Expression Assay Process Flow**

- Public/Private DB

- OligoLibrary Vendor

- KCC/TJU
- Microarray Facility

## KCC-TJU Bioarray Manufacturing

## KCC Microarray Facility for Genomic Research

**KCC Microarray Facility for Genomic Research**
**Array, Instrumentation and Software**

**BioArray**

**Hybridization**

**Signal Detection**

**Scanning**

**ScanArray software**

**QuantArray software**

## Gene Expression Technologies

**Gene Expression Technologies**
**----Targets Preparation**

## Biological Differential Gene Expression Between WT and Mutant 

**on Zebrafish 17K Expression Microarray **

## Gene expression array for genome-wide 

**Gene expression array for genome-wide **
**expression monitoring**** **

**Available in-house Microarray**
- 1) 17K Zebrafish OligoArray; 3) 23K Mouse OligoArrays
- 2) 19K Human OligoArrays;   4) Human/ Mouse miRNAArrays

## Updated Gene Expression Profiling Services Done

**Updated Gene Expression Profiling Services**** **_**Done**_

**1) Zebrafish Microarrays**
- 450 biological samples from 40 labs. in US, UK, Germany,
- Singapore, Hong-Kong have been processed
**2)** **Human Microarrays**
- 100 Samples from six labs at TJU have been processed.
**3)** **Mouse Microarrays**
- 120 Samples from Seven labs at TJU have been processed.
**4) Rat Microarray**
- 12 Samples from two labs at TJU have been processed.
**5) Human/Mouse miRNA Microarray**
- 100 Human CLL, Mouse and Rat Samples have been Processed

## Zebrafish Expression Microarray Users

**Zebrafish Expression Microarray Users**
- 450 biological samples from 40 Research Laboratories

## Slide 10

## caBIG Integrated Cancer Research Workspace

**caBIG Integrated Cancer Research Workspace**
**Contribution by KCC**

**Collection of all data pertaining to microarray experiments and distribution of experimental results**:
- The Kimmel Cancer Center is pioneering the use of a number of exclusive in-house built chips (eg. microRNA chip). It is well known that experimental design and conditions greatly influence results of microarray. The influence of all these factors will be studied as the database reaches a critical mass.
- Based on applications KCC developed for the world-wide zebra fish consortium, we will provide secure, web-based access to the large files of microarray results generated at a parent center to community of users at institutions world-wide.  Project also includes applications for microarray facility user registration and service requests (including experiment description based on MIAME standard).

## Software Architecture

**Software Architecture**

**System design**:
- Web-based databases for acquiring and retrieving user and experiment information, and controlling access to file directories containing result files to be downloaded from web.
**Component details**:
- Applications to establish user accounts and result folders, accession requests, authenticate users, distribute results.
**Relevant standards**:
- FTP, HTML, PostgreSQL, PHP, Apache, MIAME

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## 12-month work plan:

- Months **1-3**:  complete enhancements currently underway to basics applications; draft administrative and user documentation.
- Months **4-5**:  validate documentation, software and security using the zebrafish community.
- Months **6-8**:  migrate software to and train personnel at caBIG adopter sites.
- Months **9-12**: monitor use and provide updates as needed.

**caBIG Integrated Cancer Research Workspace**
**Contribution by KCC**