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We use qRT-PCR to validate differential expression and differentiation efficiencies for selected genes.
We did not observe a difference in differentiation efficiencies for all differentially expressed genes but there is clear shift of the probability mass towards deceleration.
For example, by taking into account differences in differentiation efficiencies, we can identify a more complete set of differentially expressed genes.
Other recent protocols that provide methods to purify NPCs, neurons and glia from differentiated cultures are likely to be very useful when comparing the differentiation efficiencies of different iPSC lines, when seeking to remove tumorigenic cells from cultures destined for transplantation, and in the isolation of specific cell types of interest.
The differentially expressed genes detected by DyNB as well as estimated differences in differentiation efficiencies for selected genes are validated using qRT-PCR.
In contrast, superior hiPSC cardiac differentiation efficiencies were achieved in our system without need for non-specific, toxic, and potentially mutagenic drugs.
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Thus, we studied the effect of the assumption that all genes would be affected similarly by the differential differentiation efficiency.
For instance, hiPSC lines have been shown to differentiate into neuronal lineages with variability in differentiation efficiency and in electrophysiological properties (Hu et al., 2010).
Cells of all passages were able to differentiate in vitro with close to 100% differentiation efficiency (Supplementary information, Figure S3F and S3G), suggesting that the differentiation potentials of MuSCs remained intact after serial expansions.
LY-treated cells showed reduced differentiation efficiency, whereas both ADE and recovered LY-treated ADE efficiently generated hepatocytes.
However, the necessity for further improvement in differentiation efficiency remains.
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