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A group of five differentially expressed genes were chosen for the qRT-PCR validation, which confirmed the expression pattern observed in NGS data (RC nuclear genes significantly over-expressed in OST-78 and mitochondrial genes significantly over-expressed in OST-83).
We first confirmed the expression pattern of DKK genes obtained with the microarray assay by conducting a Real-time RT-PCR analysis.
Using different methods such as semi-quantitative and quantitative-PCR we confirmed the expression pattern of a subset of genes included in our list (Figure S2).
The results confirmed the expression pattern of DE genes in the four P. digitatum samples.
The INO hybridizations confirmed the expression pattern reported previously [ 35, 79].
Real-time RT-PCR confirmed the expression pattern in seven of eight selected genes.
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Western blotting analyses confirmed the expression patterns of proteins of specific interest, and the genes encoding these proteins were further analyzed by real-time PCR.
Recent studies by Cosmopoulos et al. using real-time PCR technology confirmed the expression patterns observed in cell lines and provided further insights into the wide expression range of BART miRNAs in NPC clinical samples [11].
Semi-quantitative and quantitative PCR confirmed the expression patterns of these genes during induction/inhibition. Sequence analysis revealed the presence of conserved FoxH1/Smad2 binding elements [32], [33] in several of these genes supporting that they are direct targets.
Using quantitative real-time RT-PCR we confirmed the expression patterns obtained by microarray analysis for selected genes related to regulation of gene transcription (TIGD4, HOXC10, CHMP4B and PCAF) and cytokine secretion (SOCS7).
This confirmed the expression patterns observed in the ABA atlas.
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