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After probe purification the two separated probes were combined, mixed with hybridisation solution, denatured, and hybridised onto a 6000-feature cDNA microarray in a humidified chamber at 65°C for 16 h.
Labelled cRNA was then fragmented, mixed with hybridisation buffer, and placed on the microarray slide.
The HPV-16 E6 probe was mixed with hybridisation solution containing 50% formamide, 4 × SSC, 5% dextran sulphate, 5 × Denhardt's solution and 200 mg ml−1 ssDNA.
Labeled probes were purified by ethanol precipitation, mixed with hybridisation buffer (50% formamide, 2X SSC, 10% dextran sulfate, 1 mg/ml BSA) and denatured by incubation at 75°C for 10 min.
Chromosome enumeration probes (CEP) for chromosomes 7 (aqua), 8 (aqua), 17 (orange) and 18 (aqua) were mixed with hybridisation buffer, and denaturation and hybridisation were performed according to the manufacturer's instructions (Vysis, Downers Grove, IL, USA).
Prior to hybridisation, the labelled cRNA mixed with hybridisation buffer (0.1 M MES, 1 M NaCl, 20 m M EDTA, 0.01% Tween-20) was preheated in 5 min to 99°C and then cooled to 45°C for 5 min before loading onto the Affymetrix microarray (HG-U133A).
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In brief, samples were mixed with 40-μL hybridisation mix (3:2 hybridisation buffer/deionised formamide) and preheated at 65°C for 5 minutes.
Before hybridisation, 2 μg of each labelled cRNA product were fragmented and mixed with control targets and hybridisation buffer according to the supplier's protocol (Agilent Technologies).
Each combined probe was mixed with 45 μl of Spectral Hybridisation Buffer (Spectral Genomics), 11.3 μl of 5 M NaCl and 110 μl of room temperature isopropanol.
The reactions were then incubated at 60°C in the dark for 30 mins, chilled on ice, and mixed with 57 μL 2× GEx Hybridisation buffer (pre heated to 37°C), Following centrifugation (18000 × g for 1 min) the samples were kept on ice until loaded (103 μL) in a semi randomised order onto the microarray slides.
Spike-in experiments with mixed culture hybridisations containing isolates from two groups in various proportions were intended to evaluate the power of classification for bacterial communities.
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