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To validate the results of the microarray analysis, seven genes of biological significance were subjected to RT-qPCR and their expression levels were measured (Table S2).
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To successfully generate sufficient labelled cRNA for microarray analysis two rounds of amplification were necessary.
From Microarray analysis, two of the OP and one of the TTF clones that expressed relatively low levels of Sox2, Nanog, and Zscan4 [21] also showed heavy methylation of the Nanog promoter legion.
RNA derived from EWS-FLI-1, EWS-ERG, FUS-ERG (AML), FUS-ERG (ESFT), ERG-1 and FLI-1 expressing MPC populations were all subjected to microarray analysis; five m17k microarrays (among which 2 were dye swaps) were performed for each population, comparing cells expressing the protein of interest with the corresponding empty vector control cells.
To verify the results from the microarray analysis, nine genes with high M- and B-values were selected for real-time RT-PCR analysis of the same tissues from the same individuals, and this analysis showed a corresponding DE of six of these based on their M-values (Table 4).
For microarray analysis nine independent experiments were performed.
For microarray analysis, two independent clones from each cell line were used as biological replications.
For microarray analysis, two independent RNA samples were prepared of each condition to be examined.
Transcript level changes obtained from microarray analysis (six genes) were evaluated using quantitative real-time PCR.
For each microarray analysis three FVB and three K14E6 transgenic 6-week-old virgin female mice were employed.
For microarray analysis, four observations were analysed per sample, as on each array each cZIP probe was spotted in quadruplicate.
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