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The genetic background of the four selected TGMS lines was examined by using a genomic SNP array, RICE6K.
The bacterial chromosomal DNAs were extracted from cells that had been cultured overnight by using a genomic DNA preparation kit (Tiangen, China) with lysostaphin at 10 mg/ml and RNaseA at 25 mg/ml for the lysis step.
Genomic DNA was extracted from peripheral leukocytes by using a Genomic DNA Extraction kit (QIAamp DNA Blood Mini Kit; Qiagen, Hilden, Germany).
The genomic DNA was isolated by using a Genomic DNA Prep Kit (Tiangen Biotech Co., Ltd., Beijing, China) according to the manufacturer's instructions.
Genomic DNA was extracted from the peripheral blood from all participants by using a genomic DNA isolation kit (Genomic DNA kit; QIAGEN, Valencia, CA) according to the manufacturer's instructions.
The cells were harvested by centrifugation at 12 000 g at 10°C for 30 min. Genomic DNA was prepared by using a genomic DNA extraction kit (BioTeke, China) according to the manufacturer's instructions.
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Total genomic DNA of a liquid H. pylori B8 culture (Brucella broth, 10% FCS, streptomycin 250 mg/l) was extracted by using a genomic-tip G-500 (Qiagen, Hilden, Germany).
To construct expression plasmids of cat1+ and its point mutants, cat1+ ORF amplified by PCR using a genomic library (NBRP) as a template was cloned into pREP273-EGFP, which was generated by the replacement of multi-cloning sites together with the nmt41 promoter (Basi et al., 1993) and 3HA fragment from pSLF273 (NBRP) and the insertion of EGFP ORF in NotI and BglII sites.
To clone the gene coding for Pythium ∆-desaturase (PyDes6), a portion of gene was amplified by PCR using a genomic DNA template and degenerate primers, P14-PyDes6-F and P15-PyDes6-R (Table 3), which were designed based on conserved amino acid sequences of ∆-desaturases of several fungi, F(W/Y QQSGWLAH and (Q/N YQ(I/V)(E/D HHLFP, respectively.
For MITF genomic copy number measurements, DNA was extracted from NZM cells by using a Purelink Genomic DNA Mini Kit (Invitrogen), with 2 ng genomic DNA used as template for qPCR, and qPCR reagents and cycling conditions as described above for transcript measurement.
Genomic DNA was prepared from each blood sample by using a commercial genomic DNA extraction kit (TALENT s.r.l., Trieste, Italy).
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