Introduction to the biology and technology of DNA microarrays. Sandrine Dudoit PH 296, Section 33 10/09/2001. Biology primer. The cell. The basic unit of any living organism. It contains a complete copy of the organism's genome . Humans: trillions of cells (metazoa);
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PH 296, Section 33
other organisms like yeast: one cell (protozoa).
Larger and more complex in structure than prokariotic cells.
E.g. mammals, yeast.
Leads to the formation of gametes (egg/sperm).
males 27M, females 44M
(Broman et al., 1998);
(-NH2) and an acidic carboxyl group (-COOH).
The expression of the genetic information stored in the DNA molecule occurs in two stages:
The main types of gene expression assays:
Building the chip:
PCR PURIFICATION AND PREPARATION
Hybing the chip:
CELL CULTURE AND HARVEST
Ngai Lab arrayer , UC Berkeley
384 well plate
Contains cDNA probes
Print-tip group 1
Spotted in duplicate
Print-tip group 6
Array of bound cDNA probes
4x4 blocks = 16 print-tip groups
Binding of cDNA target samples to cDNA probes on the slide
(Lowers the Tm)
Data Analysis & Modelling
Taken from Schena & Davis
Differentially expressed genes
Sample class prediction etc.
16-bit TIFF files
(Rfg, Rbg), (Gfg, Gbg)