Pop 7 polymer for 3500 3500xl genetic analyzers

Each amplification result is checked by ethidium bromide stained agarose gel electrophoresis (2.5 %). The fragment length determination is performed with a 50 bp molecular ladder (Invitrogen). For the electrophoresis, usually a voltage of 120 V and a run time of 30 min are applied.
The STR products are separated in a 50 cm capillary on an ABI 3500 Genetic Analyzer (Applied Biosystems) using POP-7™ Polymer for 3500/3500xL Genetic Analyzers and the 3500 Data collection Software (all Applied Biosystems). Allele determination is performed with GeneMapper Software 5 (Applied Biosystems).

PCR products from the Trypanozoon sp.-positive sample, all the T. congolense-positive samples and 20 randomly selected T. vivax samples were sequenced in both directions by a commercial company. According to the protocol provided, PCR products were cleaned up with an ExoSAP-IT™ PCR Product Cleanup kit (Applied Biosystems™, Thermo Fisher Scientific) and sequenced using the BrilliantDye™ Terminator Cycle Sequencing Kit V3.1 (NimaGen B.V., Nijmegen, The Netherlands), following the manufacturers’ instructions. The labeled products were cleaned with the ZR-96 DNA Sequencing Clean-up Kit (Zymo Research, Irvine, CA, USA) and injected on to the Applied Biosystems ABI 3500XL Genetic Analyzer with a 50-cm array, using POP-7™ Polymer for 3500/3500xL Genetic Analyzers (Applied Biosystems™).
Sequence chromatogram analysis, manual clean-up, assembly and generation of census sequences were performed using the Bio Edit Sequence Alignment Editor version 7.2.5 [20 ]. The basic local alignment search tool (BLAST) [21 ] was used to identify homologous sequences in GenBank to those obtained in this study.