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(A) Validation of the microarray results in both MKN-45 and SGC-7901 cells using qRT-PCR.
Furthermore, microarray results in the current investigation showed several fold up-regulation of transcripts involved in lipid degradation.
Data obtained from EpiTYPER analysis confirmed the enrichment/methylation profiles in BMP7 and HOXD3 that were evident from the microarray results in a set of four microarray cases chosen for analysis (Figures 2, 3).
Table 2 gives the results of three independent experiments for those genes that were differentially expressed between 0 h and 6 h post treatment and is compared to the initial microarray results in Table 3.
For primary human monocytes, 19 of these 20 genes were directionally concordant with the microarray results in THP-1 cells and these same 19 were individually confirmed as significantly CO-suppressed (p<0.05, ANOVA post hoc contrast of LPS+CO vs. LPS; Table 1).
We also tested the microarray results in training sets.
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HEEBO microarray resulted in many fewer genes with a low FDR on FFPET as compared with frozen tissue (Figure 3).
On occasion this may reflect the accuracy of the selection of material for microarray, resulting in false negatives.
This is consistent with the notion that some genes are conserved across multiple regions that are interrogated by unique probes on the microarray, resulting in significantly more probes per probeset than random expectations.
By its design the multispecies probe representation on the microarray resulted in miRNA redundancy.
RNA samples were collected every 7 minutes after α-factor synchronization and hybridized with cDNA microarray, resulting in the microarray time series data with 18 time points covering two cell cycles.
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