Possible sources of dye-related signal correlation bias in two-color DNA microarray assays.
AuthorsCox WG, Beaudet MP, Agnew JY, Ruth JL
JournalAnal Biochem
PubMed ID15265729
'DNA microarray analyses commonly use two spectrally distinct fluorescent labels to simultaneously compare different mRNA pools. Signal correlation bias currently limits accepted resolution to twofold changes in gene expression. This bias was investigated by (i) examining fluorescence and absorption spectra and changes in relative fluorescence of DNAs labeled with the ... More
Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles.
AuthorsMeade SO, Chen MY, Sailor MJ, Miskelly GM,
JournalAnal Chem
PubMed ID19271746
A particle-based multiplexed DNA assay based on encoded porous SiO(2) photonic crystal disks is demonstrated. A
Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support.
AuthorsWingren C, Ingvarsson J, Dexlin L, Szul D, Borrebaeck CA,
JournalProteomics
PubMed ID17787036
Antibody-based microarray is a novel technology with great potential within high-throughput proteomics. The process of designing high-performing antibody (protein) microarrays has, however, turned out to be a challenging process. In this study, we have developed further our human recombinant single-chain variable-fragment (scFv) antibody microarray methodology by addressing two crucial technological ... More
Effects of atmospheric ozone on microarray data quality.
AuthorsFare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y
JournalAnal Chem
PubMed ID14632079
A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets designed to identify potential causes (from microarray production to array scanning) indicated that the anomaly was linked to a batch process; further work allowed us to localize the effect ... More
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome.
AuthorsHeisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD
JournalNucleic Acids Res
PubMed ID15911630
An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20,736 ... More
Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides.
AuthorsSchut GJ, Brehm SD, Datta S, Adams MW
JournalJ Bacteriol
PubMed ID12813088
The first complete-genome DNA microarray was constructed for a hyperthermophile or a nonhalophilic archaeon by using the 2,065 open reading frames (ORFs) that have been annotated in the genome of Pyrococcus furiosus (optimal growth temperature, 100 degrees C). This was used to determine relative transcript levels in cells grown at ... More
Exploring the regulation of tRNA distribution on the genomic scale.
AuthorsDittmar KA, Mobley EM, Radek AJ, Pan T
JournalJ Mol Biol
PubMed ID15001350
Though up to 20% of the total RNA in bacterial cells is tRNA, the regulation of tRNA distribution on the genomic level remains unclear. tRNA distribution is governed by four processes: transcription, processing of precursor tRNA, degradation of precursor tRNA and degradation of mature tRNA. To elucidate the relationship between ... More