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The high expression of 11 miRNAs (gma-miR164, miR167, miR168b, miR319a, miR396a, miR482b, miR482b*, miR2118a, miR2118b, miR1508a, and miR1509a) in soybean leaves has been verified by microarray analysis, as were low expression levels of miR169a, miR390c, miR1507c, and miR1510a [ 35].
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An example of the importance of the increased sensitivity and reproducibility of RNA-seq is shown by the Spp1 gene which did not show statistical significance by microarray but has been verified by qRT-PCR and in situ hybridisation (Table 2 and Figure 6).
Expression changes in all these genes, detected by DNA microarrays, have been verified by real-time polymerase chain reaction.
This was verified by a microarray analysis showing that genes which are transcriptionally activated by HIF1A were upregulated in the EGFR-CD533 expressing tumors.
The mRNA expression apparent in the captured in situ images was verified by independently derived microarray time-course analysis using Affymetrix GeneChip technology (more details can be found at http://insitu.fruitfly.org, and in Tomancak et al., 2002).
In addition to the above-mentioned origins, small RNAs of 21~24 nt from mRNAs and igRNAs increased in HT seedlings compared to those in the control lines (Additional File 4E-H), and those showing relatively high abundances were verified by a microRNA microarray analysis (Additional File 9).
Expression changes seen by microarray were verified by quantitative PCR.
The expression level of these three miRNAs detected by microarray was verified by qRT-PCR.
The expression level of the three lncRNAs measured by microarray was verified by qRT-PCR (see online supplementary results and supplementary figure S2).
The expression of seven differentially expressed genes (CDH1, EMP1, DDR1, DVL1, KRT5, KRT6, KRT17) was verified by immunohistochemistry on tissue microarrays.
The differential expression of genes obtained by microarray analysis was verified by SYBR Green real-time PCR.
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