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Briefly, an ssDNA library template consisting of a 40-nucleotide random region (N40) flanked by two constant regions was prepared and immobilized on streptavidin-coated beads (Pierce, Rockland, MA, USA) via its 5′ OH-end biotin.
Briefly, an aqueous phase was prepared from the SOLiD ePCR kit containing AmpliTaq Gold DNA Polymerase UP, buffer, MgCl2, dNTP's, amplification primers and library template.
dATP overhangs were added to the DNA using 15 µL of purified library template, dATP (1 µL 100 mM), 15 units Klenow exo- (NEB) and 2 µL NEB buffer 2. The reaction was incubated at 37°C for 30 minutes, then purified with a MinElute column and eluted in 21 µL of water.
The PEC method allowed complete coverage of the Neandertal mtDNA, using only 5 50 ng of amplified pyrosequencing library template.
In qPCR, the standard and unknown library template are amplified using two sequence-specific primers with a TaqMan fluorogenic probe labeled with FAM dye and a dye quencher.
Each library template oligo was annealed separately with the Library Primer oligo and the duplexes were filled in using Taq DNA polymerase (NEB, Ipswich, MA) as per the manufacturer's instructions.
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A procedure used to verify that 3C library templates bear the high quality required to produce superior 5C libraries is also described.
We thank Ritsuko Kazama for synthesis of the dsRNA from library templates and to Dr. Peter Bauer for assistance with ArrayScan® operation.
Library templates were clonally amplified using the Ion One Touch 2™, following the manufacturers' protocol.
Template preparation and sequencing: Library templates were prepared for sequencing using the Life Technologies Ion Xpress and Ion OneTouch protocols and reagents.
Library templates were prepared for sequencing using Illumina's cBot cluster generation system with the corresponding TruSeq PE Cluster Kits for the GA and HiSeq.
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