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Frozen tumors were manually homogenized with homogenization hammer and tissue powders were resuspended in 500 μl of PBS.
Liver biopsy samples were washed in RPMI-1640 to remove contaminating blood lymphocytes, manually homogenized with a plastic plunger, and treated with DNase (0.002%, Sigma) and collagenase IV (0.02%, Sigma) for 30 minutes, stirring at 37°C.
Heart (washed in E3 water to remove blood cells) and blood (washed in 1X PBS (Bio-Rad, Hercules, CA) and spun down at 2,000 RPM) from the wild-type zebrafish were froze in liquid nitrogen and manually homogenized with a pistil and 18- and 27-gauge needles (Tyco Healthcare/Kendall Mansfield, MA).
Similar to the RT-PCR protocol, the heart (washed in E3 water to remove blood cells) and blood (washed in 1X PBS (Bio-Rad) and spun down at 2,000 RPM) from the wild-type sibling were froze in liquid nitrogen and manually homogenized with a pistil and 18- and 27-gauge needles (Tyco Healthcare/Kendall).
The anterior midguts were then transferred to 100 µL of ice-cold MET solution (300 mM mannitol, 5 mM EGTA, 17 mM TRIS-base/HCl, pH 7.5) in a microcentrifuge tube and manually homogenized with an abrasive glass microhomogenizer during 5 min. 100 µL of ice-cold 24 mM MgCl2 were added to this preparation and the tube content was mixed.
The tissue was then manually homogenized with a potter glass.
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Tuberculous-like animal lesions were dissected and manually homogenized, then decontaminated with 4% NaOH for 15 min and centrifuged at 3,000 rpm for 15 min.
Tissue (1 × 2 mm) or cell line lysates were manually homogenized (PYREX homogenizer; VWR, Radnor, PA, USA) and prepared as previously described [ 32].
In brief, the tissue was manually homogenized by four strokes with a Teflon pestle in solution I [230 mM mannitol, 70 mM sucrose, 1 mM EGTA and 5 mM HEPES (pH 7.4)] on ice.
Fifty adult flies were manually homogenized in a microfuge tube with a small pestle in subcellular fractionation buffer (220 mM mannitol, 68 mM sucrose, 20 mM HEPES (pH 7.4), 80 mM KCl, 0.5 mM EGTA, 2 mM Mg(CH3COO 2, and Sigma protease inhibitor cocktail (Sigma #P8340)).
To avoid human factors to the bacterial community composition, the subset of sediment for DNA extraction was manually homogenized but not sieved.
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Justyna Jupowicz-Kozak
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