Next Generation Sequencing
The advent of massively parallel sequencing (next-generation sequencing, or NGS) has ushered in a new era of analysis.21. and 22. Sequencing-based approaches can be used to accurately measure mRNA abundance, novel discovery of splicing, SNPs, and even novel transcripts.21. and 22. Although NGS is a powerful technique, it is more expensive and statistically challenging than microarray analysis. Other applications of NGS are to the fields of genetics and epigenetics. Genome scale sequencing and mapping of epigenetic modification of DNA and histones can be done by combining chromatin immunoprecipitation with NGS. These ultrasensitive techniques require high-purity samples that are best derived from cell culture sources. The mouse has the great advantage that embryonic stem cell lines can be derived directly from the embryo and are an excellent source of pure trophoblast material amenable to NGS approaches. Histone methylation analysis has been applied to mouse trophoblast stem cells.23 Another epigenetic modification is DNA methylation, which can also be assessed by using an immunoprecipitation approach.24 This has been applied to trophoblast stem cell populations from the mouse.25 NGS has also been used to characterize the expression of microRNAs in the placenta.26