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2 protocols using bessman tissue pulverizer

1

Extracting and Quantifying Knee Collagen Biomarkers

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Protein was extracted from knee joints according to Nielsen et al (24 (link)) at week 0, 1, 2 and 4 after operation. Knee joints were isolated after euthanasia as described above, then immediately frozen in liquid nitrogen and stored at −80°C for use. The tibia and femur were cut 3 mm from the joint, producing samples weighing 500–700 mg. These samples were frozen in liquid nitrogen again, and transferred to a Bessman tissue pulverizer (Spectrum Chemical Manufacturing Corp.). The samples were crushed with 3 ml extraction buffer, consisting of 50 mM Tris-HCl buffer (pH 7.4), 0.1% Triton X-100, 0.1 M NaCl, 10 Mm (GM6001; Enzo Life Sciences, Inc.) and 1 tablet/10 ml buffer of Complete Mini EDTA-free protease inhibitor cocktail (Roche Diagnostics). Tissues were homogenized twice for 30 sec using an OMNI homogenizer (Omni International, Inc.) at speed level 4, then the samples were centrifuged for 10 min at 1,700 × g and 4°C, supernatants were obtained and centrifuged at 10,000 × g and 4°C. Finally, the supernatants were stored at −20°C until use.
Rat-specific commercially available ELISA kits (Elabscience®) were used to evaluate the levels of C-terminal telopeptide of type I collagen (CTX)-I (cat no. E-EL-R1456) and CTX–II (cat no. E-EL-R2554) in protein extracts collected from the knee, according to the manufacturer's instructions (24 (link)).
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2

DNA Extraction and Targeted Sequencing Protocol

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Flash frozen tissues were pulverized using a Bessman Tissue Pulverizer (Spectrum Chemical) and homogenized in Nuclei Lysis Buffer (Promega) using a gentleMACS dissociator (Miltenyi Biotec Inc). DNA was isolated using the Wizard Genomic DNA Purification Kit (Promega) according to manufacturer’s protocols. DNA quality and concentration were assessed using a Nanodrop 2000 spectrophotometer (Thermo Scientific), a Qubit dsDNA BR Assay Kit on a Qubit Fluorometer (Thermo Scientific), and the Genomic DNA ScreenTape on a 4200 TapeStation (Agilent Technologies). Libraries were prepared using the Hyper Prep Kit (KAPA Biosystems) and SureSelectXT Target Enrichment System with the JAX Cancer Treatment Profile (CTP) targeted panel of 358 related genes (Agilent Technologies) [31 (link), 32 ], according to the manufacturer’s instructions. Briefly, the protocol entails shearing the DNA using the Covaris E220 Focused-ultrasonicator (Covaris), ligating Illumina specific adapters, and PCR amplification. Amplified DNA libraries are then hybridized to the CTP probes, amplified using indexed primers, and checked for quality and concentration using the High Sensitivity D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay Kit (Thermo Scientific). Libraries were pooled and sequenced 150 bp paired-end on the NextSeq 500 (Illumina) using NextSeq v2 reagents (Illumina).
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