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So we do believe our work, by involving not only 4 different microarray platforms, but more importantly also a deep sequencing technology, does yield new knowledge.
These are transcripts not represented in any of the three microarray platforms, but this fact does not necessarily argue in favor of DGE being more sensitive.
The clustering of expression datasets seems to be independent from muscle type or microarray platforms, but rather influenced from the type of stimulus inducing atrophy.
Most data were generated using Affymetrix oligonucleotide microarray platforms, but Illumina, Agilent or non-commercial arrays were also used in some experiments (Additional File 1).
Most data were generated using Affymetrix oligonucleotide microarray platforms, but Agilent, miRCURY and non-commercial arrays were also used in some experiments.
Furthermore, we found that 305 genes (286 in MRP1 and 272 in MRP2) were present across five microarray platforms, but were not detected by MPSS, neither from the 17-bp library nor the 20-bp library.
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'Present' on one microarray platform but not the other, which are considered a separate set of discrepant results.
Thousands of expression studies employ one or the other microarray platform, but comparison of results between platforms has been difficult because of inherent differences in the array technologies.
It was anticipated that this study would serve not only to experimentally validate the microarray platform, but also shed light on the genotypic differences between the two streptomycete species, and also between the two strains of S. lividans.
The change of CXCL14 was higher according to results obtained with the microarray platform, but this is probably due to the high variation in the real-time PCR data for this gene.
Six genes (BNBD5, CASP8, COX1, INSIG1, IRAK1, and TRAF6) measured via qPCR were not present on the microarray platform but have been shown to be involved in immune response or metabolic pathways in mammary tissue [ 7, 20].
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