{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"dataset_type":["Illumina HiSeq 2000;"],"full_dataset_link":["https://ega-archive.org/datasets/EGAD00001001922"],"sample_count":["14"],"description":["EGA dataset EGAD00001001922"],"repository":["EGA"],"title":["RNA-seq from normal human tissues"],"pubmed_abstract":["Analysis of splice variants from short read RNA-seq data remains a challenging problem. Here we present a novel method for the genome-guided prediction and quantification of splice events from RNA-seq data, which enables the analysis of unannotated and complex splice events. Splice junctions and exons are predicted from reads mapped to a reference genome and are assembled into a genome-wide splice graph. Splice events are identified recursively from the graph and are quantified locally based on reads extending across the start or end of each splice variant. We assess prediction accuracy based on simulated and real RNA-seq data, and illustrate how different read aligners (GSNAP, HISAT2, STAR, TopHat2) affect prediction results. We validate our approach for quantification based on simulated data, and compare local estimates of relative splice variant usage with those from other methods (MISO, Cufflinks) based on simulated and real RNA-seq data. In a proof-of-concept study of splice variants in 16 normal human tissues (Illumina Body Map 2.0) we identify 249 internal exons that belong to known genes but are not related to annotated exons. Using independent RNA samples from 14 matched normal human tissues, we validate 9/9 of these exons by RT-PCR and 216/249 by paired-end RNA-seq (2 x 250 bp). These results indicate that de novo prediction of splice variants remains beneficial even in well-studied systems. An implementation of our method is freely available as an R/Bioconductor package [Formula: see text]."],"pubmed_title":["Prediction and Quantification of Splice Events from RNA-Seq Data."],"pubmed_authors":["Goldstein Leonard D LD, Cao Yi Y, Pau Gregoire G, Lawrence Michael M, Wu Thomas D TD, Seshagiri Somasekar S, Gentleman Robert R"],"description_synonyms":["Human, average, human being, Man (Taxonomy), Homo sapiens, Tissue., Modern Man, Modern, Whole Transcriptome Shotgun Sequencing, RNA-seq, Man, human, humans"],"name_synonyms":["Vasp, VASP, Data Set., DmelCG15112, ENHANCER OF ATNSI ACTIVITY, MENA, NDPP1, l(2)02029, Enb, enb, ENA, Ena, CG15112, ENA/VASP"],"pubmed_title_synonyms":["Whole Transcriptome Shotgun Sequencing, RNA-seq."],"pubmed_abstract_synonyms":["Ribonucleic, AV363654, human being, Materials, Procedures, determination, Mini Exon, toe syndactyly, Gene, MAP 2, RT-PCR, broad, and anogenital and renal malformations, ES2-4, EK2-2, Human, method, Techniques, MetAP 2, Homo sapiens, Method, method used in an experiment, Mini-Exon, Studies, p67, Gene Products, Whole Transcriptome Shotgun Sequencing, anogenital and renal malformations, Mood, GUC2C, E(Raf)2B, animal, Technique, Man, Non Polyadenylated, RNA Gene Products, average, study, D8Ertd419e, Man (Taxonomy), Genetic, Genomes, Moods, Tissue, stubby, MECIL, StAR, Star syndrome, procedures, STARD1, DIAR6, Non-Polyadenylated RNA, Study, l(2)05671, l(2)rK134, star, Methodological Studies, method used in an experiment., l(2)07056, STAR, CG4385, syndactyly with renal and anogenital malformations, HHT1, StARD1, Initiation factor 2-associated 67 kDa glycoprotein, RNA, l(2)k09538, wide/broad, Edg, ribose nucleic acid, l(2)21Eb, body, Affects, Modern, ribonucleic acids, RNA-seq, whole body, RNS, Procedure, MUCIL, Cistrons, results, predicted, shortened, read, Peptidase M, syndactyly, yeast nucleic acid, Ribonukleinsaeure, chemical analysis, Genetic Materials, pentosenucleic acids, Ribonucleic acids, techniques, END, START domain-containing protein 1, Genetic Material, DmelCG4385, ribonucleic acid, Acid, whole organism, Mini-Exons, Non Polyadenylated RNA, EY2-4, Non-Polyadenylated, Exon, Methodological, whole genome, Ribonucleic Acid, Methodological Study, telecanthus, human, plan specification, wide, Star/asteroid, 3.4.11.18, l(2)c00080, Material, Modern Man, Koerper, Cistron, fltr, p67eIF2, assay, ORW1, reverse transcription polymerase chain reaction, short, Luteinizing hormone-induced protein, humans, methodology"],"additional_accession":[]},"is_claimable":false,"name":"ena-DATASET-Genentech-18-02-2016-19:31:54:532-12 - samples","description":"RNA-seq from normal human tissues (2 x 250 bp)","dates":{"updated":"2017-07-26 15:39:26"},"accession":"EGAD00001001922","cross_references":{"TAXONOMY":["9606"],"pubmed":["27218464"],"EGA":["EGAC00001000055","EGAS00001001026"]}}