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fast digest buffer.
Ethanol-containing wash buffer (RPE buffer; Qiagen) was then loaded into each mini-column and centrifuged at 10,000 rpm for 1 min. Purified RNA was collected off the silica membrane using 0.025 mL of RNase free water (Qiagen) and centrifugation at 10,000 rpm for 1 min. DNA was removed by adding 0.80 mL (27.3 Kunitz units) DNase in DNA digest buffer (Qiagen) for 15 min at room temperature.
The three extracts plus the first saved digest buffer were pooled and dried completely by centrifugal lyophilization.
DNase digest buffer (10×) consists of 0.5 M Tris-HCl pH 7.5 supplemented with 0.5 mg/ml BSA.
To obtain monkey sperm and tissue genomic DNA, samples were pretreated with tissue digest buffer, supplemented with dithiothreitol and 1% SDS (for sperm only) for 3 h, followed by proteinase K lysis and phenol-chloroform extraction.
The loose pellet was resuspended in 200 μl 10X MNase digest buffer [15 mM Tris (pH 8), 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.25 M sucrose, 1 mM DTT] and subjected to MNase digestion using 20 units of MNase for 30 min at room temperature; 10 mM EDTA was added to stop the reaction.
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The gel pieces were re-hydrated in digesting buffer containing 50 mM NH4HCO3, 5 mM CaCl2 and 12.5 ng/ml trypsin at 4°C for 45 min, and incubated overnight at 37°C. 15 µl of 25 mM NH4HCO3 was added and gel pieces were centrifuged for 15 min. Two volumes of acetonitrile were added, and probes incubated at 37°C for 15 min with shaking, and the supernatants collected after centrifugation.
Precipitated P. falciparum protein preparations were dissolved in digestion buffer, digested with trypsin and LysC, and analyzed by LC/LC/MS/MS according to published protocols [22], [23].
Briefly, rat hearts were perfused with heart media (10mM HEPES, 30mM taurine, 2mM carnitine, 2mM creatine in JMEM) for 4 min at 3 ml/min and then digested with digestion buffer (1 mg/ml of collagenase II, 6.25 µM CaCl2 in 50 ml perfusion buffer) for 18 min at 3 ml/min.
Aortas were dissected, longitudinally opened, washed with PBS, cut and digested with digestion buffer (2 mg/ml collagenase type II and 0.5 mg/ml elastase in Dulbecco's modified Eagle medium (DMEM)) for 30 min at 37°C.
Lungs, livers and brains were digested with digestion buffer, 1 mg/ml collagenase (Wako Pure Industries, Ltd, Osaka, Japan), 1 mg/ml dispase (Gibco) and DNase (Sigma-Aldrich) in PBS at 37° C for 30 minutes.
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