(精选)Microarray Technologies教学课件.pptVIP

Microarray Technologies November 2006;What is your question? Hypothesis testing…;What is your question? Hypothesis generating…;AAAAAAA;An integrated system is needed for functional genomics;Nomenclature;+1;U133+ GeneChip 1.2 million probe features;Cell cycle: G2/M DNA damage checkpoint;Annotation analysis: non-obvious networks;Oligomer microarrays – Affymetrix GeneChips;Affymetrix assays $300, $375, $425 per GeneChip (single use) $400 reagents and labor, starting from total RNA 1-10 ug total RNA at 0.5 ug/ul or higher or 20 ug biotinylated, fragmented cRNA double amplification: 50ng - 1ug total RNA triple amplification: 0.5ng - 50ng total RNA Single channel detection Highest density; Agilent - GE Healthcare CodeLink Illumina – ;Affymetrix assays – prokaryotic, protozoan B. subtilis (5K, $300) E. coli (20K, $175) K12 4,358 O157:H7-EDL933 5,376 O157:H7-Sakai 5,253 CFT073 5,379 intergenic regions 714 P. aeruginosa (5.5K, $300) Plasmodium falciparum (4.3K, $300) (with Anopheles, 15K) S. aureus (3.3K, 4.8K intergenic, $275) N315, Mu50, NCTC 8325, COL Toxoplasma gondii (all transcripts, SNPs, intergenic, $175);Affymetrix assays – other interesting microbiology S. cerevisiae – all transcripts ($175) or genomic tiling ($425) S. pombe – genomic tiling ($275) Rhodobacter sphaeroides, Caulobacter crescentus, Mycobacterium tuberculosis, Group A Streptococcus Multi-Pathogen Identification (MPID) microarray that detects eighteen different pathogenic viruses, prokaryotes, and eukaryotes, including several CDC Category A and B biothreat agents. 16S rRNA small subunit array – 3,200 organisms Resequencing: Neisseria meningitidis, Bacillus anthracis, SARS;In-house microarrays – GeneMachines OmniGrid;Arrayers;Sample 1 RNA – Cy3 dye;Catalog glass slide arrays printed in-house Human 19K long oligo Mouse embryo 15K cDNA Mouse 15K long oligo Pig 11K long oligo microRNA Human mapped BAC;Printed microarray assays $30-$150 per glass slide (single use) $50-$1