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Further, the sequence of MLONG1, which was indicated by the phylogenetic clustering of MSHORT1 copies, was verified with Censor.
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Clones were screened by PCR and those carrying 2 element copies were verified by sequence analysis.
MHC class I alleles were considered part of the cDNA library after at least two copies were verified by sequencing.
The data were double entered using EPI Data 6.04 and both copies were verified.
Successful homologous integration was tested by colony PCR and single copy integration was verified via Southern blot analysis.
Specificity of MIP copy number data was verified by assessing c-myc amplification; while PIK3CA copy number appeared to be selectively increased in specific subgroups, amplification at the c-myc locus was observed at similar frequencies in all subgroups.
Expression of two copies of CEBPG and both copies of TINF2 in the NMR was verified with published RNA-seq data (Figs S5 and S6).
Integration of the CSΔN copy at the correct location was verified by PCR of PbmCherry CSΔN clone B3 parasite line using previously described primer sets ([ Coppi et al., 2011]; see Supplementary file 1 for primer sequences).
The single copy status of the UCOS was verified by removing all contigs that had multiple hits to the T. cacao genome with a e-value lower than 1E-06.
The RPPs gene-qPCR we established had a detection limit of one gene copy per reaction while its specificity was verified by sequencing.
Single copy presence of the recombined allele was verified by genomic PCR.
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