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Dudley, A., Aach, J., Steffen, M. & Church, G. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range.
Samples were processed at the University Affymetrix facility, scanning the microarrays with a GeneArray scanner and preprocessing data using RMA (Robust multiarray average) [39], [40].
Using significance analysis of microarrays with a 5% false discovery rate, 71 and 60 non-redundant transcripts were identified to be ≥2-fold up-regulated and ≤0.6-fold down-regulated, respectively, in sheared chondrocytes.
Biochemical reactions are performed 'on-chip' by overlaying the protein microarrays with a purified conjugating enzyme or extract prepared from a biological specimen (e.g. cell line or pathological specimen) and all required co-factors.
Each hypoxic time point was analyzed with at least three biological replicates using high density oligonucleotide microarrays with a minimum of four on-chip replicates (NCBI/GEO accession number GSE9331).
To establish the experimental procedure, we first probed protein microarrays with a short 36 nucleotide (nt) long RNA termed E2Bmin, which is a fragment of the Ash1 mRNA known to specifically interact with She2p [18].
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For a multi-parametric test of probe choice strategies for genotyping with ASH-based assays, we combined custom made (Agilent) high-density microarrays with an in-house multi-stringency array washer which has been described in [13].
The classification of 332 test control microarrays with an error rate of 0.6% is remarkable.
One purpose for developing this spike-in controls platform is the possibility of applying this methodology to normalize microarrays with an asymmetric representation of modulated genes.
The 3.0 and 6.0 μg/cm doses were also analyzed in gene expression microarrays with an exposure of 72 h (late effects).
This strategy allows the CTV resequencing microarray with a tiling capacity of 117 kb to encompass a sequence diversity equivalent to ten full-length CTV genomes.
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