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These probes were printed onto aldehyde slides (Genetix) using a Stanford type microarray spotter in house [50], [51].
Furthermore, in acd11, LAZ1 transcripts accumulate to levels that are almost three times higher than in wild type (microarray data not shown).
A reverse transcriptase-polymerase chain reaction (RT-PCR) was carried out to confirm the result of the microarray experiments for the genes showing different patterns of expression between the ORF type microarray and the oligo probe microarray.
The application of the GINI method to LCLs to identify transcripts harbouring germline truncating mutations is challenging due to a number of factors related to cell type, microarray sensitivity and variations in NMD efficiency.
Accordingly, we defined markers of a given cell type as those genes with probesets that are P in the corresponding pure cell type microarray, and either A or M in the other three.
In this stream, we have devised a multi-well type microarray (open system) made of plastics (dry) and gel (wet) and developed its operational method through pilot experiments such as an arrayed-colony formation, a parallel monitoring of various conditions (for crystallization), and an application to multistep reactions.
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Differences in cell type, microarrays, and populations may also be responsible for some of the large difference in estimated prevalence.
Microarray hybridization and scanning were done at the Karolinska Institute core facility for Bioinformatics and Expression Analysis, using Affymetrix HG-U133 plus 2.0 type microarrays.
For mouse testis and isolated germ cell types, microarray expression data, generated using the Affymetrix chip mouse genome 430 2.0 [18], were obtained from NCBI GEO (http://www.ncbi.nlm.nih.gov/geo/) using GEO accession number GSE4193.
Up-regulation of ErbB2 was observed in human intestinal-type microarray data, and also in our mouse data.
Transcription factors that did not show minimal expression (> 4.5 median intensity) in wild-type microarray datasets were not analyzed further.
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