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Comparison of XZ cross-sectional views of mice liver samples imaged with the two ports emphasized the advantage of our NDS device for imaging deeply inside biological samples using TPEF microscopy.
Protein-DNA was cross-linked by adding formaldehyde directly to the culture medium or to liver samples to a final concentration of 1% and then stopped 15 min later by the addition of glycine to a final concentration of 0.125 M. For mice liver samples, nuclear extracts were then prepared.
Protein lysates from mice liver samples were prepared in ice-cold lysis buffer [50 mM Tris HCl (pH = 8.0), 1.0 mM ethylenediaminetetraacetic acid, 150 mM NaCl, 0.1% NP-40 and 1 mM phenylmethylsulfonyl fluoride, supplemented with 1× Complete protease inhibitor cocktail (Roche)].
Mice liver samples of the 1.2.32 (Tg [HBV 1.3 genome] Chi32) lineage (HCC negative and HCC positive) were kindly donated by Ulrike Protzer, Institute of Virology, TU Munich, Germany.
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Lunularin (chemical purity >97%, determined by NMR) for i.p. injections and the analysis of resveratrol and its metabolites in mouse liver samples at the MRI Karlsruhe (Germany) was prepared as described previously in a modular synthesis41.
Resveratrol and the microbial metabolites dihydroresveratrol and lunularin were quantified in mouse liver samples by using a UHPLC-MS/MS method that meets the validation criteria of the FDA.
Total RNA was harvested from mouse liver samples as described for microarray RNA isolation.
Mouse liver samples were homogenized in RIPA buffer (50mM Tris-HCl, 150mM NaCl, 2mM EDTA, 0.5% Sodium deoxycholate, 1% Igepal CA-630, 5mM DTT), containing protease inhibitor (SIGMA).
Mouse liver samples were blinded and shipped on ice.
Mouse liver samples were retrieved from 11-week-old male C57BL/6 J mice.
A total of 14 mouse liver samples were used to prepare a pooled sample.
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