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Only samples with RNA Quality Indicator (RQI) >7.5 were kept for the microarray analyses (for most samples: RQI >8.5/9).
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"Keep — for the moment".
At each stage 3 replicates were used for microarray analysis and another was kept for RT-PCR validation of the microarray results.
After eliminating spots flagged as bad, not found or absent and those with a signal intensity that did not surpass twofold their background signal, only 2598 and 3148 spots were kept for further analysis in microarray 1 and 2 respectively.
After filtering on gene expression level and gene annotation, 13,021 genes (57.3% of the genes present in the microarray) were kept for further analysis.
Genes in the two datasets were matched by Entrez ID, and only genes that were common to both datasets, and detected to be expressed in the microarray, were kept for further analysis.
Genes in the two datasets were matched by Entrez ID, and only genes that were common to both sets, and detected to be expressed in the microarray, were kept for analysis.
The remainder was kept for future research.
The explants were kept for 24 hours.
RNA samples were split: one fraction saved for fluorescent labeling (see below) and the other kept unlabeled for NanoSIMS microarray analysis.
Raw data files for the microarray have been uploaded to ArrayExpress under the accession no.
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