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An alternative for accurate, quantitative global expression profiling is serial analysis of gene expression (SAGE; [ 8]), which in contrast to microarray hybridization allows the detection of new transcripts.
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Microarray-based comparative genomic hybridization allows the construction of high-resolution maps of genome-wide copy number alterations.
Shotgun DNA microarray hybridization analyses allowed for transcriptome comparison of these promastigotes with amastigotes obtained by infection of the U937 cell line.
Quantitative real-time RT-PCR (qRT-PCR) confirmation of microarray hybridization results allowed a more accurate determination of groups of similar expression.
Prior to microarray hybridization, each microarray was allowed to equilibrate at 4C for at least 15 min and then pre-blocked in 25 30 mL Blocking Buffer (1X PBS; 1% BSA w/v; 1 mM DTT; 50 µg/mL E.coli tRNA; 20 µg/mL heparin) at 4°C for 2 hours with gentle shaking.
Aliquots of all samples were normalized to 150 ng/μl to allow microarray hybridization.
However, obtaining data of gene expression via sequencing rather than using specific microarray hybridization would not only allow detection of novel transcripts and retrieve species-specific data, but would reduce bias in gene expression profiling from possible cross-species hybridization mismatches [ 16, 18, 19].
Finally, gene expression data resulting from microarray hybridizations does not allow exploration of the potential role of protein modification in the structure of multi-subunit complexes.
Chromatin immunoprecipitation combined with either microarray hybridization (ChIP-chip) or sequencing (ChIP-seq) allows to determine genomic association of DNA binding proteins and to analyze epigenetic regulation [1], [2], [3].
Following the experimental validation of our cross-hybridization procedure, we have written a novel program, OliD, which allows the automatic design of long oligonucleotides for microarray hybridization experiments.
aaUTP incorporation allows for the coupling of Cy3 or Cy5 dyes (GE biosciences) onto aRNA for microarray hybridization.
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