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In dual color labeling experiments, we observed that Cy5-labeled Gas6 (58 nM) and Dylight488-labeled Protein S (55 nM) bound to the same subpopulation of cells, with no reduction in binding when compared with single label only controls.
In the first color labeling, CD25 molecules were labeled with biotinylated anti-human CD25 antibody and then with streptavidin-conjugated QD 605.
In the second color labeling, CD4 (or CD8) were labeled with rabbit anti-human CD4 (or CD8) and then with anti-rabbit IgG (H + L -conjugated QD 655.
cDNA was labeled with the Quick Amp 2 Color Labeling Kit (Agilent Technologies, Santa Clara, CA) and hybridized to Agilent 2×22 k oligo microarrays containing probes for nearly the complete C. elegans genome.
Briefly, 1 µg of genomic DNA was used for dual color labeling (inverse Cy3/Cy5).
Color labeling for the testing set was based on prediction agreement (by Multi-class SVM and cuPSSM methods).
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Starting with 10 μg of aRNA, double strand cDNA synthesis was carried out using SuperScript Double-Stranded cDNA Synthesis kit (Invitrogen, Carlsbad, CA) using random hexamer primer (Promega, Madison, WI) followed by Dual-Color Labeling Kit (Roche NimbleGen, Madison, WI) using 1 O.D. CY-labeled random nonomer primer per 1 μg double-stranded cDNA in triplicate.
For FACS, highly crossreactive protein binders were selected using a two-color labeling scheme based on fluorescent-conjugated detection reagents for expression (anti-c-myc epitope tag) and binding to ELR+ CXC chemokine (anti-biotin) at recommended dilutions (Supplementary Table 12).
These reagents allow two-color labeling of cell populations for identification after mixing and co-culture.
Total RNAs (350 ng) were amplified and labeled using a two-color labeling protocol with the Low Input Linear RNA amplification kit (p/n 5184-3523), according to the manufacturer's recommendations (Agilent).
We incubated the developing larvae successively with two calcium-binding dyes, Alizarin Red S and Calcein (green), with a period of washing out between the two applications, and we examined the two-color labeling pattern after the second application.
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