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To control for variation in individual probe hybridization efficiency and fluorescence intensity, mechanically sheared whole genomic DNA was used as a template for cRNA hybridization on a separate array.
Second, representations prepared from the two parents were compared on a separate array.
Each sample from an individual bird was hybridized on a separate array along with a universal reference sample of genomic DNA pooled from 4 zebra finches (two males and two females) labeled with Cy5.
A full factorial dye-swap design was implemented, where a target from each animal's mRNA was hybridised on a separate array with all animals from different strains, and each array was repeated with the corresponding dyes switched, to correct for dye biases.
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RNA from each heifer was hybridized to a separate array.
RNA from each pig was hybridised to a separate array.
Future array based methods could include mRNA profiling and a separate array for profiling the genotype of the corresponding probe sets and their surrounding regions.
Fosmids were prepared by the same method and printed as a separate array.
Thirty genes were identified as being differentially expressed in autistic brain samples relative to matched tissue controls on a combination of 2 separate array platforms containing 588 or 9374 cDNA probes, indicating that autism is associated with multiple disturbances in gene expression.
Each cell line was analysed on two separate arrays with the dyes reversed, providing a total of four (genes printed in duplicates on each array) measurements per gene and cell line.
To test the inter-array PCR variation, a PRI-lock probe mixture ligated on a 10-fold dilution series of P. infestans target was assayed in triplicate on three separate arrays.
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