earray 5.0 Create your own Custom Microarray Design

Transcription

1 earray 5.0 Create your own Custom Microarray Design

2 earray 5.x Overview Session Summary Session Summary Agilent Genomics Microarray Solution earray Functional Overview Gene Expression Probe Design CGH High Definition (HD) databases Page 2

3 earray 5.x Agilent Microarray Solution SurePrint tm Technology Agilent Array Technology at a Glance: - In situ oligo synthesis process - Ink-jet printing/phosphoramidite chemistry - Array design defined by electronic file The Agilent Advantage: - Accurate probe synthesis and placement - Great feature morphology - Print any probe sequence between 25-60bp - Multiple file formats to choose from SurePrint technology is uniquely suited to leverage a flexible, webbased approach to creating custom microarrays. Page 3

4 earray 5.x Agilent Microarray Solution Agilent s Microarray Portfolio Agilent provides microarray solutions for a comprehensive set of genomic applications earray currently/ soon will provide a custom component to these applications. DNA RNA acgh/ CNV CH 3 ChIP GX mirna OLS Copy number Cancer Research Cytogenetics Population Studies Methylation Discover and monitor epigenetic changes that play a role in cellular processes Transcription Factors Elucidate the role that protein-dna interaction plays in transcription, replication, and repair Gene Expression Explore gene transcription on a genome-wide basis across a variety of model systems RNA interference Profile micrornas and explore the role they play in gene regulation Oligo Library Synthesis (OLS) Gene Silencing Protein Mutagenesis Whole Gene Synthesis Genome Partitioning Now Now Now Now 2008 Now Page 4

5 earray 5.x Agilent Microarray Solution Agilent Solution Workflow Agilent provides custom solutions, not just products Scanning and Feature Extraction Data Analysis & Viewers earray earray is the first step in Agilent s Microarray solution offering Automated Hyb & Wash Sample Preparation Arrays Sample QC Amplification & Labeling Page 5

6 earray 5.x Functional Overview Function Highlights earray is a secure, web based application that allows you to: Create custom microarray designs Examine Agilent Catalog Content Work collaboratively with others and share designs Search High Definition (HD) CGH/LA Databases Design Custom Probes for Gene Expression (GE) Support High Density Array formats (1 244K, 2 105K, 4 44K, 8 15K) for Free! Page 6

7 earray 5.x Functional Overview The Content Paradigm Agilent Probe 001 Annotation Agilent Probe 002 Annotation Agilent Probe 003 Annotation Agilent Domain Probes Probe Groups Microarray Design Microarray Slide Your Probe 001 Your Probe 002 Your Probe 003 Your Probe 004 Your Probe 005 Your Probe 006 Your WorkGroup Page 7

8 earray 5.x Functional Overview Content Tools Ways to Search Content Keyword searches :GB accession numbers, Gene Symbols, Probe IDs Text string searches (description field) Gene Ontology (GO) Categories Chromosomal Locations; Cytoband IDs Tools and Links Links to NCBI Genbank Pages Filter Probes Based upon metrics Compare Probe Groups Links to EMBL and UCSC genomic browsers Page 8

9 earray 5.x Functional Overview The Workgroup Paradigm Agilent Domain Agilent Catalog HD CGH Probe Database HD ChiP Probe Database Superadmin Your WorkGroup Collaboration Space Other WorkGroup Admin Users Probes, Probe Groups, Microarray Designs Probes, Probe Groups, Microarray Designs Page 9

10 earray 5.x Functional Overview Collaboration Space Example Page 10

11 earray 5.x Functional Overview The Array Creation Process earray provides an easy way of managing the array creation process. Search Agilent Probes Design Probes Create Probe Groups Create Microarray Designs Submit to Manufacture Order Arrays Upload Probes Download Design Files Page 11

12 earray 5.x Functional Overview The UI Design Wizards Design Wizards Takes you through the most common scenarios for creating a microarray design, from start to finish. Page 12

13 earray 5.x Gene Expression Probe Design Probe Design Options Options Same algorithms as catalog probes tm matched methodology also available Probe Length between 25-60bp Upload FASTA file or Genbank IDs Page 13

14 earray 5.x Gene Expression Probe Design Probe Design Process Input Sequence Output Probes Preprocessing Masking Candidate Probes Similarity Search Thermo Calc. Hyperlink to process Page 14

15 earray 5.x Gene Expression Probe Design Other Gene Expression Tools GE Transcript Tiling GE Probe Check Page 15

16 earray 5.x Gene Expression Probe Design Research Spotlight Ramsey et al., 2007 Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design Ramsey et al., 2007 BMC Genomics, 8:423 Background Boyce Thompson Institute for Plant Research, Ithaca, NY Studying the green peach aphid, Myzus persicae (Sulzer), a world-wide insect pest capable of infesting more than 40 plant families Methods Constructed 16 cdna libraries from aphid tissue Sequenced 26K ESTs from libraries ESTs Clustered and Annotated SNPs in contig 254, cathepsin B, a putative gut-specific cysteine protease. Three SNPs were validated by sequencing genomic DNA. Three SNPs in the gene result in one silent change (Leu-Leu), one substitution of a negatively charged amino acid for an aliphatic amino acid (Ala-Glu) and one substitution of an aromatic for an aliphatic amino acid (Leu- Phe) in the green M. persicae lineages (G006 and F001) relative to the red USDA lineage. Results Use resulting targets to design an 8 X 15K gene expression microarray in earray for use in future research.

17 earray 5.x CGH Array Design CGH HD Search Options Custom CGH HD Arrays can be used to resolve genomic insertions and/or deletions at defined genomic locations CGH HD Database Probes Probes Tm matched to 80 C (Probes between bp long) Searchable by Genomic Intervals and Genbank accession numbers Probes are unique to the target genome Page 17

18 earray 5.x CGH Array Design CGH High Definition Databases Comparative Genomic Hybridization (CGH) HD Database: Species Probe# Density Build Annotation Human 8.4 Million 200 bp NCBI Build 36 Mouse 7.2 Million 200 bp NCBI Build 36 Rat 6.9 Million 200 bp UCSC Rn4 Chromatin Immuno precipitation (ChIP) HD Database: Species Probe# Density Build Annotation Human 23.8 Million <100 bp NCBI Build 36 Mouse 27.4 Million <100 bp NCBI Build 36 Rat 22.1 Million <100 bp UCSC Rn4 In addition to A. gambiae; A. thaliana; C. elegans; D. melanogaster; S. cerevisiae (~ 1.0 M each) Page 18

19 earray 5.x CGH Array Design Research Spotlight Shen et al., 2007 Development of a focused oligonucleotide-array comparative genomic hybridization chip for clinical diagnosis of genomic imbalance. Shen et al., 2007 Clinical Chemistry 53: Background Department of Laboratory Medicine, Children's Hospital Boston Studying microdeletion and microduplication syndromes and how they contribute to developmental disorders Methods Selected > mer oligonucleotide features from Agilent's earray probe library to interrogate all subtelomeric and pericentromeric regions and 95 additional clinically relevant regions for a total of 179 loci Results Focused CGH array detected all known regions of genomic imbalance in 51 validation samples with 100% concordance and an excellent signalto-noise ratio

20 earray 5.x Summary earray earray is a web based application that enables the creation of custom microarrays leveraging Agilent s oligonucleotide in situ synthesis microarray platform in support of several application workflows, including CGH, ChIP and Gene Expression. Page 20

21 The End Questions? Page 21