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To estimate the yield of library and its relative amplification value, library DNA was quantitated using a Nanodrop and serial dilutions of 1.25 nM library were compared to a reference library by real-time PCR using primers complementary to the library adapters.
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These were corrected as ssDNA pools 5′-GGGAGCTCAGAATAAACGCTCAA-N35-TTCGACATGAGGCCCGGATC-3′ 5′-GGGAGCTCAGAATAAACGCTCAA-N35-TTCGACATGAGGCCCGGATC-3′ 5′-GGGAGCTCAGAATAAACGCTCAA-N35-TTCGACATGAGGCCCGGATC-3′ 5′-GGGAGCTCAGAATAAACGCTCAA-N35-TTCGACATGAGGCCCGGATC-3′ 5′-GGGAGCTCAGAATAAACGCTCAA-N35-TTCGACATGAGGCCCGGATC-3′
Typically the abundance of each shRNA vector has been determined by PCR amplification across a DNA sequence unique to that vector (a so-called DNA barcode) followed by hybridization of the PCR product to a custom microarray containing oligonucleotides complementary to the various barcodes present in the library.
After hybridization, non-specific DNA fragments are washed away, while the library DNA fragments complementary to the probes are subsequently recovered by an elution step.
For a typical library construction, an oligonucleotide library is designed complementary to the ssDNA with flanking regions corresponding to the phagemid vector.
Fifteen rounds of PCR amplification were performed to enrich the adapter modified cDNA library using primers complementary to the ends of the adapters.
Ten rounds of PCR amplification were performed to enrich the adapter-modified cDNA library using primers complementary to the ends of the adapters.
The screening of this library was complementary to our previous microsatellite marker development which was done with DOR364, a Mesoamerican source used to create un-enriched, small insert libraries [ 33] as well as marker development in Brazil which has used Perola and IAC-UNA, two other Mesoamerican varieties [ 17, 21, 22].
Shortly, adapter sequences were linked to the complementary DNA (cDNA) samples, the library was size selected (300-350bp), amplifiedfied by polymerase chain reaction (PCR).
To obtain ≥1 μg of metagenomic complementary DNA (cDNA) for the library required for the nanopore sequencing protocol, randomly amplified cDNA was generated using a primer-extension pre-amplification method (Round A/B) as described previously [ 19– 219.
Exon capture involves the hybridization of genomic libraries to short oligonucleotide baits complementary to complete or partial exomes printed on a microarray [ 7] or attached to magnetic beads in solution [ 11].
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