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The Balanced PCR products were evaluated on a 1% Agarose gel and measured over 3500 bases (data not shown).
We also found that the dependence of the ligation efficiency on mRNA length was negligible up to 800 bases (data not shown).
The amounts of aRNA recovered after two amplification cycles was 16 20 μg and the predominant size was 300 600 bases, but extending up to 2000 bases (data not shown).
The 2 sequenced swine-origin subtype H3N2 isolates from Fair E differed from each other by 32 nt, indicating increased genetic diversity among the influenza A viruses circulating among the swine at Fair E compared with that at the other fairs from which isolates from swine differed by ≤7 bases (data not shown).
Column-purified samples showed a smear ranging from 400 to 6000 bp (figure 4B), guanidinium purified samples showed a smear from 100 to over 6000 nt (figure 4C), and samples purified with LiCl had preservation of larger products with a variable recovery of transcripts less than 200 bases (data not shown).
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In the adenomatous crypts, Ki67 expression tended to be highest at the top of each crypt, relatively low in the central region and intermediate at the base (data not shown).
The comparison of base classifier performances indicates SVM and random forest outperforms other base classifiers (data not shown), and ensemble classifiers generally perform better than base classifiers, especially the boosting algorithms using decision trees as the base learner.
During our independent experiments, we found that iPS induction in FBS based media was slower than in KSR based media (data not shown), consistent with recent report (Okada et al., 2010).
This effect was more pronounced for ANOLEA and CHARMM based predictors which are more sensitive to small coordinate changes than ProsaII based predictors, data not shown.
It was also attempted to use de Bruijn graph based assemblers such as velvet [ 26] and SOAP [ 33] for 454 read based transcriptome assembly, however the contig length distribution was inferior to the overlap based assemblers (data not shown) and the analysis was not pursued further.
We confirmed the identity of the four archaeal proteins in the purified exosome by separation on SDS polyacrylamide gel (SDS-PAGE), followed by in-gel protease digestion, electrospray mass spectrometry, and data base matching (data not shown).
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