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The company started off with making custom plasmids, or molecular cloning, as the first steps towards its goal of letting users write custom experiments directly.
These devices can be customized both mechanically and functionally as the user can simply select the operation mode on the switch or alter the code to perform custom experiments.
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This paper provides a framework for embedding a custom experiment project within an existing course.
The scatterplot in Figure 6A depicts, for each of the 5776 genomic regions co-bound by both GABPα and CREB1 in A549 cells, the best binding score predicted by any PWM derived from our custom PBM experiments that included CREB1 (x-axis), and the best score predicted by any PWM derived from experiments using only one of the two proteins (y-axis).
These data provide a tool for designing custom microarray experiments related to annotated functions [ 41].
Based on these results, we propose a protocol to identify and confirm shorter exonic CNVs combining computational prediction algorithms and custom aCGH experiments.
Additionally, also genes that showed a differential expression in five out of nine, six out of nine and seven out of nine custom array experiments might still be potential players in melanocytic tumorigenesis.
To this end, we created position weight matrix (PWM) DNA binding models from each of our custom PBM experiments and used them to score all genomic sequences bound by both GABPα and CREB1 in the same cell type (i.e., GABPα+CREB1 peaks; see Materials and Methods).
These results prove the accuracy and reliability of the custom capture experiment.
Compared with the custom array experiment using the direct labelling method, we found that 91% (n=157) of the analysable genes showed a similar expression pattern and only one of these genes showed an aberrant differential expression than was found by Affymetrix arrays.
An interesting observation is that HXB2-yeast spike set has slightly lower average signals than the custom-made experiment specific control probes, indicating that custom-made, genome specific, negative controls might be better for background signal estimation than these standard spike-sets.
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