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We extracted DNA from 30 mg of bone powder and converted it into an Illumina sequencing library using DNA adaptors that carry project-specific barcodes.
We drilled 50 70 mg of bone powder from each specimen and extracted DNA using a modified version of the protocol from71: samples were incubated overnight with the extraction buffer at 42 °C instead of at 37 °C, the bone powder was pelleted out of suspension, and the supernatant concentrated down to 150 200 μl for each sample using 30 kDa Amicon centrifugal filter unit (Millipore).
In total, we generated 5.3 Gb of Neandertal DNA sequence from about 400 mg of bone powder.
The bones samples were dissolved using ca. 70 mg of bone sample in 6 mL HNO3, 3 mL H2O2 and 1 mL HCl, all concentrated and all of analytical grades.
From below the surface of each of these bones, we removed 50 to 100 mg of bone powder using a sterile dentistry drill in our Leipzig clean-room facility.
Approximately 200 mg of bone was incubated overnight in 3 ml of 0.5 M EDTA with 0.5 mg/ml Proteinase K and 0.1% Triton X-100.
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These results confirm and extend those of Chan et al. who found no effect of simvastatin 20 mg on bone ALP or urine NTX-I [ 16] in hypercholesterolemic Chinese subjects.
DNA was extracted from 250 400 mg samples of bone or tooth.
Between 100 and 400 mg of fine bone powder as well as a "reagent blank" were incubated and gently shaken in 3 ml of extraction buffer (EDTA 0.5 M, 0.5% lauryl-sarcosinate) and 100 µl of proteinase K (20 mg/ml) overnight at 56°C.
PCR amplifications were in 20 µl reaction volumes containing the following: 1× PCR buffer (10 mM TrisHCl [pH 8.8]; 50 mM KCl; 0.1% Triton X-100), 4.0 mM MgCl2, 200 µM dNTPs, 1.0 µM of the primer mix, 0.5 units of Platinum Taq polymerase (Invitrogen), and 7.5 µl DNA, equating to ∼15 mg of starting bone powder, as suggested by Krause et al. [37].
About 500 mg of cortical bone was removed, powdered and extracted as described [ 20, 22].
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