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When tagging samples, if an original image's quality was mediocre, the image was duplicated; one copy marked as "blurred" and the other marked as "sharp," with both images used for training.
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We conducted a single 454 sequencing run using one PicoTiterPlate divided into two regions, each with 10 MID tagged samples.
Following the manufacturer's protocol, we tagged each sample with the proprietary capture reagent, mixed equal amounts from both tagged samples (WT or AP, grown in vitro or in vivo), and used the mixed samples to hybridize with the probes on the microarray slides overnight.
Samples were run on 1.3 regions of a 4 regions Picotiterplate for the 454 Titanium system (per region 14 MID tagged samples were pooled) and processed according to the small volume emulsion PCR.
One is pooling of tagged samples with each individual tagged by a unique short barcode.
Multiple isobaric tag samples were normalized by comparing the median protein ratios for the reference channel.
MageComet features an auto complete widget that helps curators tag samples with consistent annotations.
Each sample was labeled with a different isobaric tag (6 per experimental comparison) and the tagged samples were then combined.
One possible reason is that due to the "sticky" nature of tagged samples, negative control regions may sometimes be called as significantly enriched (statistically) in ChIPed DNA from tagged samples when compared to WT samples, creating false-positives.
Fragmented, tagged samples from different individuals are mixed in equal amounts to form a single pool of DNA molecules.
Therefore, another approach was chosen [ 35] and reduced representation libraries (RRL) were built: a genomic library with tagged samples (AFLP fragments) and a transcriptomic library (cDNA fragments).
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