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To ascertain the quality of RNA used in microarray analysis, similar datasets of breast cancer tissue generated with the same CodeLink platform were downloaded (GEO accession numbers: GSM144855 to GSM144858) and compared with the liver microarray datasets.
As revealed by microarray analysis, similar genes were induced by both cytokines in Huh-7 cells (IL-28A: 117 genes; IL-29: 111 genes), many of them playing a role in antiviral immunity.
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Microarray analysis yielded similar pathways to those seen with the transcriptional analysis, in particular ETC, for both DOX and DMNQ (Figure 3B).
However, levels of the TNF transcript as determined by microarray analysis were similar to those previously obtained by qPCR [12], validating monocyte activation by CEsHUT and inhibition by HDL in the 3 experiments.
Remarkably, the expression of the NHEJ components Atku70 and AtligIV increased 2 to 4-fold in WT, which was barely detectable in microarray analysis and similar to that induced after a 10-fold lower IR dose [110], suggesting poor IR-regulation compared to HR genes in WT.
Comparison of the results from real-time RT-PCR with those from microarray analysis revealed similar patterns of expression.
Comparison of these genes suggests that the general trends in expression observed by microarray analysis are similar but somewhat muted as compared to that observed by RT-PCR.
For all these genes we performed validation results by independent RT-qPCR on 39 cases of PA, which confirmed the data obtained during microarray analysis with similar expression differences.
The screen developed has rich potential if extended to include other ion channels or genome-wide microarray analysis, and similar investigation of gene induction by NGF could show nociceptor-specific mechanosensitive channels.
Notably, the mRNA encoding the proteasome subunit Rpn5p, which was found in both complexes by microarray analysis with similar enrichment factors (eIF3e = 5.1; eIF3m = 8.1) was also confirmed as being associated with both eIF3 complexes by RT-PCR (Fig. 5B).
The principle behind microarray analysis is similar to that of traditional hybridization using nitrocellulose membranes [ 2]: When fluorescently-labeled sample (target) is applied to the array-bound features (probes), complementary regions of probe and target DNA will anneal to form a stable duplex.
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