Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays.
We compared different hybridization conditions of oligonucleotide-based DNA microarray to acquire optimized and reliable microarray data. Several parameters were evaluated at different hybridization conditions, including signal-to-background (S:B) ratios, signal dynamic range, usable spots, and reproducibility. Statistical analysis showed that better results were obtained when spotted, presynthesized long oligonucleotide arrays were blocked with succinic anhydride and hybridized at 42 degrees C in the presence of 50% formamide.
Tsai
Mong-Hsun
MH
Radiation Oncology Sciences Program, Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 8717 Grovemont Cr., Room 109J, Gaithersburg, MD 20878, USA.
Yan
Hailing
H
Chen
Xi
X
Chandramouli
G V R
GV
Zhao
Shuping
S
Coffin
Deborah
D
Coleman
C Norman
CN
Mitchell
James B
JB
Chuang
Eric Y
EY
D000818:Animals; D005559:Formamides / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods / Q000592:standards; D006358:Hot Temperature; D006801:Humans; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods / Q000592:standards; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013387:Succinic Anhydrides / Q000737:chemistry
D005559:Formamides; D009838:Oligodeoxyribonucleotides; D013387:Succinic Anhydrides; C031066:formamide; C031801:succinic anhydride