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To test whether the association of MYCN at sites of hypermethylation is correlated with reduced expression of genes, we have analyzed the Kelly and SK-N-AS cell lines using the NimbleGen expression microarray platform.
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Double-stranded cDNA was cleaned and labeled using the NimbleGen genes expression analysis protocol (NimbleGen Systems, Madison, WI, USA).
Using The NimbleGen platform with high-density expression arrays, Batista et al. [ 8] compared the transcriptomes of granulosa-like cells overexpressing, or not, FOXL2, one of the earliest ovarian markers which, together with its targets, can serve as a model to study ovarian development and function in normal and pathological conditions.
In a genome-wide expression analysis using the NimbleGen microarray platform, of Auxin/Indole-3-Acetic Acid (Aux/IAA) and Auxin Response Factor (ARF) in Populus (Populus trichocarpa clone Nisqually-1), the genes in a subgroup of Aux/IAA showed differential expression among different tissue types [ 18].
With the current release, queries can be performed against the grape co-expression network inferred using the Nimblegen grape genome arrays (default) or the grape Affymetrix Genechip arrays.
Microarray was carried out using the NimbleGen microarray service.
Images were extracted and processed using NimbleScan v2.4 software and analyzed using the NimbleGen commercial pipeline.
cDNA was labeled using the NimbleGen Dual-Color Labeling Kit (NimbleGen) according to manufacturer's protocol.
The probes were designed and printed by Nimblegen using the Nimblegen probe design pipeline previously published (Roche Nimblegen Probe design Fundaments 2008).
After incubation, arrays were washed using the NimbleGen Wash Buffer Kit and dried using the NimbleGen Slide Dryer.
500 1000 ng of isolated DNA was labeled using the NimbleGen Dual-Color Labeling Kit (NimbleGen) according to manufacturer's protocol.
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