Thus CMs were obtained from HCM and control S3-iPS4 iPSCs, followed by whole transcriptome sequencing using an Ion Torrent Sequencer (Life Technologies).
This is the first report of development and validation of a comprehensive set of genic-SSR markers in pigeonpea by deep transcriptome sequencing using next generation sequencing technology.
Additionally, one could align the initially unaligned reads against expressed sequence tags that were obtained by earlier transcriptome sequencing using an accurate read alignment tool, such as Subread [ 64].
Transcriptome sequencing using the 454 GS-FLX Titanium platform (454 Life Sciences, Branford, Connecticut, USA) was performed by GATC Biotech (Konstanz, Germany).
Variants were identified from transcriptome sequencing using GATK [ 23, 24].
Large scale SNP discovery and genotyping were done using two high-throughput methods: First, transcriptome sequencing using 3'-anchored cDNA 454 sequencing and genotyping using Illumina GoldenGate assays, and second using genotyping-by-sequencing RAD-seq.
These efforts were also preceded or accompanied by transcriptome sequencing efforts using different technologies [61 64], in support of gene prediction [65], but also for depicting transcriptional processes and define cell functionality in physiological, pathological, or stress conditions.
For instance, SNP identification by transcriptome sequencing or using known EST sequence data showed that approximately 90% of identified SNP loci correspond to hemi-SNPs [ 17], resulting in a large number of heterozygous signals in genotyping analyses with SNP arrays [ 16, 38].
The volume of sequence data generated by transcriptome sequencing provides the opportunity for larger scale sequence comparisons than previously possible using the few full length bat genes available or by comparison with the limited whole genome sequence data.
