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Before the analysis, data for 58 of the 384 SNPs were removed because they displayed a high degree of heterozygosity on some microarray plates but not on others and were therefore considered to be unreliable.
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As an initial screening for substrate identification the different JAK2 proteins were incubated on PamChip® 96 microarray plates.
Biolog phenotypic microarray plates PM1 through PM20, were inoculated according to the manufacturer's specifications, and incubated at 37°C for 72 hours.
Initially the microarray plates were tested for quality by an M plot and the data normalized by the RMA method from the Affy package.
Metabolic and sensitivity profiles of CCH were obtained using 11 phenotype microarray plates, where cells were incubated for 25 h (CCH25), and 3 additional hormone/immune plates, where cells were incubated for 44 h (CCH44).
We inspected the sample 2 standard dataset by creating the color image of M values in the format of the original microarray plate, and found blurred traces largely stretched over the plate.
The microarray plate was imaged by the SNPscope reader (Beckman Coulter, Fullerton, CA).
To increase our knowledge of diversity among these archival strains, we scored for metabolic changes using Biolog Phenotype Microarray™ plates (ES, PM1 and PM3) followed by plating on MacConkey agar base supplemented with a variety of sugars.
We had paper plates but nobody cared.
Cells after ethidium bromide treatment were plated on YPD and YPG plates, and cells that grew on YPD plates but not on YPG plates were selected.
Phenotype microarray (PM) plates (Biolog Inc., Hayward, California) were used to examine carbon utilization of S. oneidensis MR-1 and the deletion mutant strains in duplicate.
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