Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes

ABSTRACT: Deep sequencing of transcriptomes allows quantitative and qualitative analysis of many RNA species in a sample, with parallel comparison of expression levels, splicing variants, natural antisense transcripts, RNA editing and transcriptional start and stop sites the ideal goal. By computational modeling, we show how libraries of multiple insert sizes combined with strand-specific, paired-end (SS-PE) sequencing can increase the information gained on alternative splicing, especially in higher eukaryotes. Despite the benefits of gaining SS-PE data with paired ends of varying distance, the standard Illumina protocol allows only non-strand-specific, paired-end sequencing with a single insert size. Here, we modify the Illumina RNA ligation protocol to allow SS-PE sequencing by using a custom pre-

ORGANISM(S): Caenorhabditis elegans

SUBMITTER: Philipp Drewe 

PROVIDER: E-GEOD-40507 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress