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Twenty micrograms of cRNA was fragmented at 94°C for 35 minutes in fragmentation buffer (GeneChip® Sample Cleanup Module) and hybridised onto HG-U133A GeneChip® arrays (Affymetrix) for 16 hours at 45°C.
Biotin-labeled cRNA was purified using the GeneChip Cleanup Module prior to fragmenting to a size of 35 200 bases by incubating at 94°C for 35 minutes in fragmentation buffer (40 mM Tris-acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate).
The cRNA target (20 ug) was incubated at 94°C for 35 minutes in fragmentation buffer (Tris, MgOAc, KOAc).
The cRNA target (20 μg) was incubated at 94°C for 35 minutes in fragmentation buffer (tris base, magnesium acetate, potassium acetate).
Degraded RNA was prepared by treatment at 65°C for 15 minutes in fragmentation buffer (40 mM Tris acetate, pH 8.1, 100 mM potassium acetate, 30 mM magnesium acetate).
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The resulting cRNA product was cleaned (GeneChip Sample Cleanup Module; Affymetrix), and a 20-μg aliquot was heated at 94°C for 35 minutes in the fragmentation buffer provided with the cleanup module (Affymetrix).
The labeled cRNA was purified using RNeasy columns (Qiagen, Valencia, CA) and fragmented in fragmentation buffer at 94°C for 35 minutes.
11 μg of cRNA were then fragmented in fragmentation buffer (Affymetrix) at 95°C for 35 minutes and hybridized for 16 h at 45°C onto MOE430A microarrays (Affymetrix).
Bound RNA was fragmented by incubation at 94 °C for eight (8) minutes in 19.5 μl of fragmentation buffer (Illumina).
The slight drop in fragmentation efficiency at 10 Hz, 4 minutes is most likely explained by fiber damage occurring consistently at these higher energy settings.
Twenty µg of biotin-labeled RNA was fragmented to ∼200 bp size by incubating in fragmentation buffer containing 200 mM Tris-acetate pH 8.2, 500 mM potassium acetate and 500 mM magnesium acetate for 35 minutes at 94°C prior to hybridization.
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