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Studies were assessed for quality, with only high quality studies included for analysis.
Extracted RNA was assessed for quality with a Lab-on-a-chip Bioanalyzer 2100 (Agilent Technologies).
The final libraries were assessed for quality with the Bioanalyzer (Agilent, Santa Clara, CA) to determine final library size and concentration.
Labeled cRNA was purified using the GeneChip Sample Cleanup Module, quantified by UV spectrophotometry and assessed for quality with the Bioanalyzer 2100.
Then 15 μg labeled cRNA was fragmented into 50 to 200 bp fragments and assessed for quality with a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).
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Total RNA and the resulting cDNA library were assessed for quality and concentration with Agilent Bionalyzer, using their high sensitivity DNA chip.
Tapes will be rated by an independent rater and assessed for quality of delivery and compliance with treatment protocols.
The single stranded cDNA was assessed for quality using spectrophotometric methods in combination with the Agilent Bioanalyzer.
Total RNA was extracted using TRI reagent (Sigma), assessed for quality on an Agilent 2100 Bioanalyzer with the RNA 6000 Nano chips, and subjected to two rounds of poly(A) selection using Poly(A Purist technology (Ambion).
Short sequencing reads were extracted using fastq-dump and assessed for quality using fastQC (see URLs).
Draft genome bins were then assessed for quality, contamination, and completeness using CheckM v.1.0.566.
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