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The suitable amplification procedure consisted of an initial denaturation at 94°C for 5 min; denaturation at 94°C for 1 min, annealing at 35°C for 1 min, extension at 72°C for 90 s and in total five cycles; denaturation at 94°C for 1 min, annealing at 50°C for 1 min, extension at 72°C for 90 s and in total 35 cycles; extension at 72°C for 8 min; preservation at 4°C.
This is actually higher than in a comparable Drosophila screen where enhancer detection without a suitable amplification system was about 2% [ 9].
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To determine if the extracted DNA samples were suitable for amplification, an 18SrRNA gene fragment was first amplified, which showed significant fluorescent amplifications in all 22 DNA samples (data not shown).
Oligonucleotide primers suitable for amplification of corresponding mRNA were employed for reverse transcriptase-polymerase chain reaction (RT-PCR) amplifications using as template total RNA extracted from female SG, female carcasses (i.e. adult females from which SG had been dissected), and whole adult males.
To these, the extraction method of May and Ristaino (15: RisNC), which was reported to be suitable for amplification from minute amounts of a more than 150 year old herbarium specimen, a commercial DNA extraction kit especially designed for extraction of ancient DNA (AncA), and a simple genomic DNA extraction kit (Fermentas, FerG) were added.
The GS20 Library Prep Kit was used per manufacturer's protocol to make a ssDNA library suitable for amplification using the GS20 emPCR Kit and then prepared for sequencing on the Genome Sequencer 20 Instrument using the GS 20 Sequencing Kit.
In order to increase the probability to obtain suitable DNA amplification of the targeted marker, the philosophy underlying PHYLORPH is to target the most closely related genomic resources available (same class or order, as possible) to the non-model species targeted.
Due to this degradation, FFPE tissue is not suitable for amplification of large DNA segments.
These chromosome-specific SSRs are therefore considered suitable for amplification in tetraploid cotton.
Furthermore, the PCR products produced were within the range suitable for amplification by PCR from archival DNA.
Primers suitable for amplification for each transcript were designed using an online tool from Invitrogen, OligoPerfect™ Designer (http://tools.invitrogen.com/content.cfm?pageid=9716).
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