Centromeric K111 s were amplified by PCR with the primers P1, which binds to K111 flanking centromeric repeat CER:D22Z3, and primer P4, which binds to the K111 gag gene to produce a ~ 1.6 Kb amplification product [25 (link)]. The PCR was carried out using the Expand Long Range dNTPack PCR kit (Roche Applied Science, Indianapolis, IN). PCR was performed at a final volume of 50 μl using an initial step of 92 °C for 2 min, followed by 35 PCR cycles consisting of denaturation at 92 °C for 15 s, annealing at 55 °C for 30 s, and extension at 68 °C for 5 min. Amplification products were confirmed by sequencing [25 (link)].
Kaplan M.H., Kaminski M., Estes J.M., Gitlin S.D., Zahn J., Elder J.T., Tejasvi T., Gensterblum E., Sawalha A.H., McGowan J.P., Dosik M.H., Direskeneli H., Direskeneli G.S., Adebamowo S.N., Adebamowo C.A., Sajadi M, & Contreras-Galindo R. (2019). Structural variation of centromeric endogenous retroviruses in human populations and their impact on cutaneous T-cell lymphoma, Sézary syndrome, and HIV infection. BMC Medical Genomics, 12, 58.
Other organizations :
University of Michigan–Ann Arbor, Feinstein Institute for Medical Research, Hematology Oncology Associates, Marmara University, Istanbul University, University of Maryland, Baltimore
Expand Long Range dNTPack PCR kit (Roche Applied Science, Indianapolis, IN) used for PCR
PCR conditions: initial step of 92 °C for 2 min, followed by 35 PCR cycles consisting of denaturation at 92 °C for 15 s, annealing at 55 °C for 30 s, and extension at 68 °C for 5 min
controls
Amplification products were confirmed by sequencing
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