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For cDNA library construction, fruit and flower RNAs were pooled, respectively, by mixing equal amount of RNA from each developmental stage.
A reference pool was made by mixing equal amount of RNA from the parasites collected at 6 hours interval throughout the 48 hours life cycle and was labeled with Cy3 (GE-Amersham).
The leaf samples of each accession were collected by mixing equal amount of leaf tissues from 6 plants from National Germplasm Guangzhou Sweetpotato Nursery located in Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
For an initial scan of the whole marker set, a DNA pool was established for each group by mixing equal amount of genomic DNA prepared from individuals within each group.
Artificial inoculation was carried out using fresh bacterial inoculum, prepared by mixing equal amount of two fuscans isolates 12 and 118, and two no-fuscans isolates 18 and 98 with spores at the concentration of 108 CFU/ml.
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The tolerant pool (T-pool) was made by mixing equal amounts of DNA from 20 extreme cold-tolerant RILs with a PSST above 0.90, and the sensitive pool (S-pool) was made by mixing equal amounts of DNA from 20 extreme cold-sensitive RILs with a PSST below 0.63 (Additional file 2: Table S1).
We used several standard controls on all plates that were genotyped, including the reference genome line Nipponbare, 93-11, an F1 between Nipponbare and 93-11 (kindly supplied by Guo-liang Wang of Ohio State University) and a "pseudo F1" that was prepared by mixing equal amounts of genomic DNA from Nipponbare and 93-11.
Monoclonal mouse anti-human IgG was prepared by mixing equal amounts of mouse anti-human IgG1 (51 mg/ml), IgG2 (22 mg/ml), IgG3 (16 mg/ml) and IgG4 (24 mg/ml).
Samples were prepared by mixing equal amounts of matrix (α-cyano-4-hydroxycinnamic acid from Sigma) and sample, each dissolved in 50% acetonitrile and 50% 0.1% trifluororacetic acid (TFA).
NO produced by the adhered PEC was measured by mixing equal amounts of supernatant with Griess reagent (1% sulfanilimide in 2.5% H3PO4 and 0.1% napthylethylenediamine dihydrochloride in 2.5% H3PO4 mixed in a 1∶1 ratio just prior to assay).
Total RNA was extracted separately for each tissue type used, including heart, gill, nerve, muscle, and whole crabs, and a pooled total RNA was constructed by mixing equal amounts of total RNA from each of the tissue specific pools.
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