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The white crosses represent the locations where the MAST data are rejected using the quality check procedure in this study.
Spikes or vibration effect and eddy currents due to the commutation of strong diffusion gradient pulses, were corrected using the Quality Check pipeline of the Connectomist toolbox used in this study (Duclap et al., 2012).
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History information was used to do the quality check for species name as well.
RNA that passed the quality check using an Agilent Bioanalyzer were used for microarray analysis using Mouse WG-6 v2.0 Expression BeadChip Kits (Illumina).
The RNA was quantified using the NanoDrop ND-1000 (TherMA Scientific, Mandand the quality checked using the Bioanalyzer 2100 (Agilent, CA) according to manufacturer's instructions.
The total RNA was re-suspended in RNase-free water, quantified using a spectrophotometer and the quality checked on 1% agarose gels.
The RNA was quantified using the NanoDrop nd-1000 (TherMA Scientific, MA, USA) and the quality checked using the Bioanalyzer 2100 (Agilent, CA, USA) according to manufacturer's directions.
Total RNA was isolated using Ultraspec II RNA kit (AMS Bioscience, Abingdon, UK) and the quality checked using an Agilent bioanalyzer (Agilent Technologies UK, Stockport, UK) for the RNA required for the microarray analysis and on a nanodrop (Thermo Scientific, Wilmington, DE, USA) for the samples to be used for QPCR.
Total RNA concentration was calculated from the absorbance at 260 nm and the quality checked using BioAnalyzer Agilent technologies (Santa Clara, CA, USA).
GO annotations that pass our standard quality checks and the quality checks using the GO Consortium produced GO annotation file checking script are made public on the AgBase website.
FastQC v0.10.1 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used for quality check.
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