GEO

In the recent past, microarray technology has been extensively used by the scientific community. Consequently, over the years, there has been a lot of generation of data related to gene expression. This data is scattered and is not easily available for public use. For easing the accessibility to this data, the National Center for Biotechnology Information (NCBI) has formulated the Gene Expression Omnibus or GEO. It is a data repository facility which includes data on gene expression from varied sources.

Microarray probe design parameters

For 25-35 mers

Parameter	Minimum Value	Maximum Value	Default Value	Unit
Probe Length	10	99	30	bases
Probe Length tolerance	0	15	3
Probe Target Tm	40	99	63	°C
Probe Tm Tolerance (+)	0.1	99	5
Hairpin Max ÄG	0.1	99.9	4	Kcal/mol
Self Dimer ÄG	0.1	99.9	7	Kcal/mol
Run/Repeat	2	99	4	bases

For 35-45 mers

Parameter	Minimum Value	Maximum Value	Default Value	Unit
Probe Length	10	99	40	bases
Probe Length tolerance	0	15	3
Probe Target Tm	40	99	70	°C
Probe Tm Tolerance (+)	0.1	99	5
Hairpin Max ÄG	0.1	99.9	6	Kcal/mol
Self Dimer ÄG	0.1	99.9	8	Kcal/mol
Run/Repeat	2	99	5	bases

For 65-75 mers

Parameter	Minimum Value	Maximum Value	Default Value	Unit
Probe Length	10	99	70	bases
Probe Length tolerance	0	15	3
Probe Target Tm	40	99	75	°C
Probe Tm Tolerance (+/- above)	0.1	99	5
Hairpin Max ÄG	0.1	99.9	6	Kcal/mol
Self Dimer ÄG	0.1	99.9	8	Kcal/mol
Run/Repeat	2	99	6	bases

Other Parameters

• Probe Location
  1. 3' end bias: The oligos chosen should be towards the 3' end of the gene i.e. Default : 3' end.
  2. The oligos should be designed by default within 999 bases of 3' end. The range can be from 0 to 1500 bases.

• The oligos should be free of cross homology (i.e They should be BLAST searched against the appropriate genome category).

DNA Microarray with Array Designer: Array Designer is an exceptional software to design highly specific oligos for expression and SNP genotyping microarray experiments.