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Briefly, 100 ng of genomic DNA were labeled by a random primer reaction during two hours.
One half μg of digested and ethanol-purified DNA and normal female reference DNA were labeled by a random primer reaction with Cy3-dUTP and Cy5-dUTP (Amersham Pharmacia Biotech Inch)., respectively, and co-hybridized to the array slides in 48 hours at 37°C by use of an automated hybridization station (GeneTAC, Genomic Solutions/Perkin Elmer) and our established protocol [ 50].
Each cDNA probe was purified by agarose gel electrophoresis, recovered by using a QIAEX gel extraction kit (QIAGEN Inc., Chatsworth, CA, USA), and radiolabelled by a random primer technique with a commercially available kit (Amersham Life Science Inc., Arlington Heights, IL, USA).
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In brief, TAP treatment was followed by ligation with an excess of 5′ adapter (Illumina TruSeq Small RNA kit) and by reverse transcription using a random primer (RPO primer: 5′CCTTGGCACCCGAGAATTCCANNNNNN-3′).
Oligonucleotide 1 and 2 were also used to generate non-radioactive and radioactive probes by utilizing the PCR DIG Probe Synthesis Kit from Roche Diagnostics (Mannheim, Germany) or by α-P]dNTP incorporation using a Random Primers Labeling System (Gibco-BRL, Cergy-Pontoise, France), according to the supplier's protocol.
Then the first strand cDNA was synthesized by a random hexamer-primer using the mRNA fragments as templates.
The membrane was analysed using indirect end-labelling with a probe generated by random primer labelling from a 151 bp PCR product prepared using the primers 5'-tgtgcaaattccaactaaagga-3' and 5'-ggcgataatttatcatgttttcc-3'.
IS CR and sul2 PCR product amplified with primers CRF/CRFF-r were labeled with P-ATP by random primer extension by using a commercially available kit (Stratagene, Amsterdam, the Netherlands) according to the manufacturer's instructions.
The cRNA (3 μg) was reverse transcribed in the first-strand cDNA synthesis step by using a random hexamer primer, followed by RNase H-mediated second-strand cDNA synthesis in replicates.
With this technique, target RNAs of ten potato viruses were reversal transcribed by random primer in a single reaction, then subjected to LDR and asymmetric labeling PCR as template, finally, the MRLP amplicons were analyzed by microarray hybridization and subsequent scanning.
In brief, 2 µg of genomic DNA from test sample (GK) and 2 µg from reference (Wistar) were digested by AluI/RsaI and labeled by random primer, incorporating Cy5 (red) and Cy3 (green) fluorescent dyes.
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