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While analyzing the DNA methylome of multiple myeloma (MM), a plasma cell neoplasm, by whole-genome bisulfite sequencing and high-density arrays, we observed a highly heterogeneous pattern globally characterized by regional DNA hypermethylation embedded in extensive hypomethylation.
By semi quantitative scoring of the intensity of staining of those tissue arrays we observed that both the frequency and the positivity for C4BP were highest in AMI compared to hypertrophy and aorta stenosis (Figure 1B).
In the current study, using TaqMan PCR arrays, we observed a global downregulation of miRNAs in both human and mouse metastatic sarcomas.
Using the Affymetrix present call classification in FlyAtlas (4 out of 4 arrays), we observed that 3 out of the 5 retrogenes are expressed in testis in D. melanogaster as opposed to only one described in [ 21].
In line with and expanding earlier results using smaller 225-antigen arrays, we observed on the > 540-antigen arrays specific and differential serum autoantibody reactivities to COMP, clusterin, osteoglycin, apolipoprotein E, histones H2A and H2B, serine protease 11, and other candidate antigens.
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Consistent with the array, we observed that METH caused substantial increases in ATF3 mRNA (Fig. 4D).
Upon hybridization of the λ-exonuclease resistant DNA preparation to the array, we observed that the peak profile obtained with these two preparations was almost indistinguishable from that obtained without λ-exonuclease treatment (Figure 2), indicating that the peak profile observed did not arise from contaminating DNA.
Upon hybridization of the 0.7 1.5 kb nascent DNA (test DNA) and similarly size sheared total DNA (reference DNA) to the tiling array, we observed a strong short-range autocorrelation among neighboring probes (Fraction 10 12, Fig. 1A), which was absent in the input\input hybridization (self-self, Fig. 1A).
Using the printed glycan array, we observed an unexpectedly rich spectrum of AGA with similar amounts in plasma and ascites.
In contrast to the SWS2-LWS array, we observed considerable variation in opsin gene content for the RH2 opsins.
Among 39,936 spots in the array we observed up-regulation of 580 genes (p < 0.05) while 457 genes were down regulated (p < 0.05, Table 2, Additional file 3).
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