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To overcome the challenge of probe design for templates of random sequence, we adapted the universal template (UT) approach where a probe-binding sequence is appended to one of the PCR primers [ 10].
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We review the template fabrication of random arrays of nanoband electrodes on highly ordered graphite surfaces and on carbon nanotubes, acoustic methods of fabricating random arrays of metal nanoparticles on electrode surfaces, and numerical methods of simulating and modelling the electrochemical processes that occur at such arrays.
Subsequently, mRNA was fragmented to short fragments to be used as templates for random hexamer-primed synthesis of first-strand cDNA by fragmentation buffer.
Fragmentation buffer was added and the resulting 200~300 bp fragments were used as templates for random hexamer-primer synthesis of first-strand cDNAs.
After a 10 min remodeling by SWI/SNF, nucleosomes were repositioned from the center of the template to random locations along the entire sequence.
Sequencing of the unamplified SL confirmed that all of the possible combinations of template random nucleotide sequences are represented.
Importantly, the same DG markers were sequenced consistently at high or low relative frequencies from different RILs, indicating that variation in depth of sequencing was intrinsic to the DG template rather than a result of random variation or due to variation in template preparation.
The results of resequencing activities suggested that MspJI successfully generates DNA templates with a moderate level of random fragmentation.
We performed a reverse transcription reaction with 300 ng of RNA as template, using an equal ratio of Random Hexamers and Oligo dT primers and the SuperScript III Kit (Invitrogen).
Unlike ETA, this is done by choosing multiple semi-random templates of just three residues, biased towards conserved, non-hydrophobic, structurally neighboring residues with minimal overlap with other chosen templates.
Reverse transcription was carried out with the use of 0.5 μg of template RNA, random hexamer primers, and smart MMLV reverse transcriptase (Clontech).
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