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Microarray scanning and feature extraction was performed at ICBR using an Agilent G2505B Microarray Scanner and Agilent Feature Extraction Software v9.5.
MBS designed and constructed the hyperspectral microarray scanning and wrote all data acquisition software.
Labeling of RNA, hybridization to microarrays as well as microarray scanning, and quantile normalization of the raw data were done externally (Source BioScience imaGenes, Berlin, Germany).
AKC performed RNA and protein isolation and quantification, RNA processing and microarray scanning and data mining, realtime quantitative RT-PCR and Western blot validation experiments, confocal immunofluorescence and histological analysis of suture tissues, and drafted the paper.
We would like to thank Dr. Hans Mollenkopf from the Max Planck Institute for Infection Biology Berlin (MPI-IB) and Julia Jarells from the Max Planck Institute of Cell Biology and Genetics Dresden (MPI-CBG) for providing facilities and advise for microarray scanning and data extraction.
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However, detection of this mRNA on the microarray scan and its subsequent verification by RT-PCR analysis indicates the sensitivity of the microarray assay.
Sample labeling, hybridization to microarrays, scanning and calculation of normalized expression levels were carried out at the Microarray Resource, Boston University School of Medicine, Boston, MA.
Thus, using these microarray scanning procedures and engineering modifications, ozone degradation of the Cy5 dye was minimized.
After labeling, the cRNA of pooled samples was hybridized to MOE 430A microarrays, scanned and statistically evaluated.
Different aspects of this technology such as experimental design, total RNA isolation, double-stranded cDNA synthesis, complementary RNA synthesis, target hybridization and microarray scanning, post-translational modification of CREB and data interpretation and bioinformatic analysis are discussed.
Microarray scanning, feature extraction and normalization procedures were performed as described for the cell line experiment.
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