SPELL - Nematode

Citation	Smith LM, Hartmann L, Drewe P, Bohnert R, Kahles A, Lanz C, Ratsch G. Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. RNA Biol, 2012.
PubMed ID	22614838
Short Description	Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes. GEO Record: GSE40507 Platform: GPL13776 Download gene-centric, log2 transformed data: WBPaper00041119.ce.rs.csv
# of Conditions	4
Full Description	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-adenylated 3' adaptor. We generate parallel libraries with differing insert sizes to aid deconvolution of alternative splicing events and to characterize the extent and distribution of natural antisense transcription in C. elegans. Despite stringent requirements for detection of alternative splicing, our data increases the number of intron retention and exon skipping events annotated in the Wormbase genome annotations by 127% and 121%, respectively. We show that parallel libraries with a range of insert sizes increase transcriptomic information gained by sequencing and that by current established benchmarks our protocol gives competitive results with respect to library quality. Experimental Details: RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP015332.SRX181515 RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP015332.SRX181516 RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP015332.SRX181517 RNASeq.elegans.WBStrain00000001.WBls:0000002.Hermaphrodite.WBbt:0007833.SRP015332.SRX181518.
Tags	Method: RNAseq, Species: Caenorhabditis elegans, Topic: gene expression - general