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Correlations of expression levels of the various transcripts were studied using Pearson correlation (Table 2).
The cycle number at which the various transcripts were detectable (threshold cycle, CT) was compared with housekeeping CT, referred to as ΔCT.
The relative amounts of 36B4 and the various transcripts were calculated using the following formula: relative amounts of mRNA = 1/2 CT - Time X - CT -Time 0), where C T-Time X is the C T number at one experiment time point, and C T-Time 0 is the C T number at time 0. The levels of 36B4 and the various transcripts at time 0 were arbitrarily assigned as 100%.
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The fold difference in various transcripts was calculated by the ΔΔCT method using Hprt as an internal control [ 27].
The fold difference in various transcripts was calculated by the ΔΔCT method using Hprt as the internal control.
Expression of various transcripts was investigated at 3-4 days post seeding of cells, since preliminary experiments indicated that expression of MMP-2 and MMP-9 mRNA is dependent on the cell density as it has been reported previously [ 39].
Induction of IGF2 transcripts by SYT-SSX1 within each cell population was comparable when different primer sets were used and various IGF2 transcripts were selected.
Firstly, RNAs were isolated from different tissues of plants at several stages of development growing under various conditions, and transcripts were sequenced using GS-FLX next-generation sequeNGSng (NGS) technologies.
However, interferon-lambda-1 is a pseudogene in mouse, while interferon-lambda-4 is a pseudogene in both species [18] (experimental cloning of human IFNL4 was attempted in our company and several spliced transcripts were found in various tissues [data not shown]; however, 5' RACE experiments did not reveal an ORF with a Met, which led us to conclude that human IFNL4 is a pseudogene).
As a control experiment, the transcription start site and RNA level of the various lhrÁ-lacZ transcripts were tested by primer extension analysis using a lacZ-specific primer.
Heatmaps illustrating expression patterns of various subgroups of transcripts were generated in R as described by Severin et al. [ 26].
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