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Based on this observation, it was hypothesized that if conditions were sufficiently optimized, it should be possible to take the pre-amplification pool template and directly perform the barcoding PCR step, without an intermediate second-stage amplification on the Access Array chip.
With this information, the Construct Design Module can compute a script of pipetting instructions for the Tecan liquid handler to perform all the necessary liquid handling events needed to pool template DNA with amplimers, polymerase, and buffers within individual wells of a 96-well PCR plate.
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Thermal cycler PCR conditions were 95°C for 15 min followed by 42 cycles of 95°C for 40 sec., 58°C for 2 00 min., 72°C for 1 30 min. and finally 72°C for 10 min. PCR amplification from pGIPZ plasmid pool templates was essentially performed in the same way as from genomic DNA, only that the copy number was adjusted to 1,500 copies per equimolar pGIPZ construct (6 pg/100 μl PCR).
Comparison of SNPs identified from pooled templates with those from individual sequences revealed a very low false positive rate.
This synthetic library (termed SL) provides a library of random sequences that reflect the complete pool of template sequences available prior to amplification.
Finally, in order to optimize PCR conditions, different primer concentrations were tested by real-time RT-PCR with the cDNA pool as template.
cDNAs encoding the entire open reading frame (ORF) of three S. mansoni 2DBD-NRs (Sm2DBDα, Sm2DBDβ and Sm2DBDγ) were isolated by a PCR strategy using a S. mansoni female worm cDNA library (pBluescript SK phagemid) pool as template DNA [ 6, 22].
The general strategy for NGS-TILLING is to amplify multiple target exons from pools of template DNAs, and then to pool and barcode all of the targets from a single library pool for sequencing.
From the BAC library, we selected three Jamaica BAC clones covering the HWC2 region by PCR screening using the most tightly linked DNA markers of HWC2 at that point using three-dimensional BAC pools as template DNA.
Brett Berk of Vanity Fair praised the episode for "not only retreating into the series's standard, flailing, everybody-in-the-pool narrative template, or filling this metaphorical slough with more leaden tropes than Richard Serra circa 1968, but by having the results be precisely the inevitabilities we all knew would occur".
Portions of the inoculums were diluted in PBS and spread on TSA blood plates containing chloramphenicol (6 µg/ml), ampicillin (1 µg/ml) and gentamycin (2 µg/ml) to verify the infection dose and to generate input pool DNA templates for subsequent PCR detection of tagged mutants.
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