{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["6(7)"],"submitter":["Siebert S"],"pubmed_abstract":["We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particula"],"journal":["PloS one"],"pagination":["e22953"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC3146525"],"repository":["biostudies-literature"],"pubmed_title":["Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows."],"pmcid":["PMC3146525"],"pubmed_authors":["Shaner N","Goetz F","Smith SA","Siebert S","Tintori SC","Helm RR","Dunn CW","Robinson MD","Haddock SH"],"additional_accession":[]},"is_claimable":false,"name":"Differential gene expression in the siphonophore Nanomia bijuga (Cnidaria) assessed with multiple next-generation sequencing workflows.","description":"We investigated differential gene expression between functionally specialized feeding polyps and swimming medusae in the siphonophore Nanomia bijuga (Cnidaria) with a hybrid long-read/short-read sequencing strategy. We assembled a set of partial gene reference sequences from long-read data (Roche 454), and generated short-read sequences from replicated tissue samples that were mapped to the references to quantify expression. We collected and compared expression data with three short-read expression workflows that differ in sample preparation, sequencing technology, and mapping tools. These workflows were Illumina mRNA-Seq, which generates sequence reads from random locations along each transcript, and two tag-based approaches, SOLiD SAGE and Helicos DGE, which generate reads from particula","dates":{"release":"2011-01-01T00:00:00Z","publication":"2011","modification":"2026-04-16T01:10:56.14Z","creation":"2025-07-13T03:04:40.751Z"},"accession":"S-EPMC3146525","cross_references":{"pubmed":["21829563"],"doi":["10.1371/journal.pone.0022953"]}}