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The dilution curve was created using a cDNA pool of each of the test cDNAs.
Primer efficiency was determined using a cDNA pool with serial dilutions (1, 10−1, 10−2 and 10−3).
The amplification efficiency (E) for all primers was determined using a cDNA pool dilution series from all culture conditions and the Relative Expression Software Tool (REST) for calculations [ 55].
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One microgram of total RNA was used to create a cDNA pool of ~30 μg utilizing the High Capacity RNA-to-cDNA Kit (Applied Biosystems, #4387406, San Francisco, CA, USA).
PCR efficiency was calculated from standard curves that were generated using serial dilutions of a cDNA pool of all worm samples.
The isolation of the medfly homologs of the cellularization genes sry α and nullo by degenerate primer PCR using an embryonic cDNA pool was not successful [ 9].
Primers were designed on the basis of the homologous EST sequences and used to amplify from a cDNA pool of Golden Promise a full-length cDNA for HvCCA1 and a partial gene for HvPRR1 (Additional file 1: Table S1).
Total RNA (500 ng) was isolated from frozen fungal mycelia using the TRI Reagent kit (Molecular Research Center, Cincinnati, OH, USA) and a cDNA pool was generated using the SMART™ PCR cDNA synthesis kit (Clontech, Palo Alto, CA, USA) per the manufacturer's instructions.
Each plate for PCR run included the cDNA samples from malignant and non-malignant tissue pairs, a non-template control, samples of a cDNA pool used as calibrator, and another one for precision control.
(E) Standard curves were generated to calculate the RT-qPCR efficiency using 10-fold serial dilutions from a cDNA pool [ 17].
Stomach poly(A)+ RNA (2 μg) was isolated with the "QuickPrep Micro mRNA purification kit" (GE Healthcare) and a cDNA pool was synthesized using the "First Strand cDNA Synthesis kit for RT-PCR (AMV)" (Roche) with the oligo (dT 17RIRO primer adaptor [ 25].
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