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In the adPEO patients the relationship between mtDNA copy number and structural maintenance is not as straight-forward as could be inferred from the data from the developmental changes in childhood.
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These arguments make use of empirical data from both the developmental and the animal cognition literature.
Most sequence data were from the developmental time course experiment, which surveyed berry samples collected from three individuals of the O'Neal cultivar, an early ripening variety of southern highbush blueberry that is widely grown in North Carolina and other southern US states.
We obtained the paired end sequence data from the fly developmental modENCODE project and calculated expression levels of isoforms from FlyBase 5.45 for all developmental stages using the same protocol as used in the original modENCODE analysis (see Methods).
Direct interview data from the Early Developmental Stages of Psychopathology Study (EDSP), a 4 5 year prospective-longitudinal design based on a representative community sample of adolescents and young adults, aged 14 24 years at baseline, are used.
The RNA-seq data from the same developmental stages were put together.
The same evaluation procedure applied to data from the whole developmental series was tested on different sample combinations which, in our understanding would represent plausible experimental contexts.
Because not all polymorphic differences are due to structural changes in the gene itself, we also used expression data from the intraerythrocytic developmental cycle.
We obtained the paired end sequence data from the fly developmental modENCODE project [ 22] from the European Nucleotide Archive [ 52] and calculated expression levels of isoforms from FlyBase 5.45 for all developmental stages.
Expression of the 221 PxSP and PxSPH genes was profiled using RNA-seq data from the different developmental stages of the insecticide-susceptible strain (Fuzhou-S) including eggs, larvae, pupae and adults.
Read coverage and methylation ratio scores (see Materials and Methods for methylation ratio calculation) from these data were compared with our MBD-seq data from the same developmental stage.
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