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cDNA samples from each biological replicate were labeled twice with a green channel fluorescence dye (Cy3) and twice with a red fluorescence channel dye (Alexa 647).
RNA samples from each biological replicate were labeled twice, once with each dye, to control for dye-specific effects on the hybridizations.
The labeled cRNA of the EGF-treated and the control samples from each biological replicate were labeled with alternate dyes and co-hybridized in duplicate with dye reversal to the Agilent Human 4 × 44K 60-mer oligo microarray according to the manufacturer's protocol.
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50 µg protein per biological replicate were labelled with 2D-DIGE Cy3 Dye for control or Cy5 Dye for kairomone exposed group (GE Healthcare Life Sciences) following the protocol of the manufacturer.
Each biological replicate was labeled with a unique tag.
A "dye-flip" approach was used to minimize dye-specific bias, where two biological replicates were labeled with Cy3 and hybridized with Cy5-labelled reference and vice versa (four replicates).
Biological replicates were labeled alternately using Cy3 or Cy5 to guard against dye-bias.
Three sets of cultures (biological replicates) were labeled with Cy3 and Cy5 and hybridized onto Whole Mouse Genome Oligonucleotide Microarrays (Agilent) containing 41,174 probes representing 20,163 genes [58].
Briefly, RNA samples form 3 biological replicates were labeled and hybridized on Affymetrix Drosophila Genome 2.0 Array.
For each treatment, same amounts of RNA from three independent biological replicates were labeled and hybridized according to Agilent's One-Color Microarray-Based Gene Expression Analysis (OAK Lab GmBH, Hennigdorf, Germany).
The assays were done on 5 µg of total RNA samples from two biological replicates (each replicate consisted of pooled RNA sample originating from 15 animals) of Tribolium female and male adults from different treatments, where one biological replicate was labelled with Cy3 and the other with Cy5.
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