Datasets

Title	Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus
Organism
Number of Samples	6
Release Date	2019/03/11 00:00
Sequencing Types
Protocol Details

Title
Authors	Wang X,You X,Langer JD,Hou J,Rupprecht F,Vlatkovic I,Quedenau C,Tushev G,Epstein I,Schaefke B,Sun W,Fang L,Li G,Hu Y,Schuman EM,Chen W
Journal	Nature communications
Publication Date	2019 Nov 1
Abstract	Gene annotation is a critical resource in genomics research. Many computational approaches have been developed to assemble transcriptomes based on high-throughput short-read sequencing, however, only with limited accuracy. Here, we combine next-generation and third-generation sequencing to reconstruct a full-length transcriptome in the rat hippocampus, which is further validated using independent 5´ and 3´-end profiling approaches. In total, we detect 28,268 full-length transcripts (FLTs), covering 6,380 RefSeq genes and 849 unannotated loci. Based on these FLTs, we discover co-occurring alternative RNA processing events. Integrating with polysome profiling and ribosome footprinting data, we predict isoform-specific translational status and reconstruct an open reading frame (ORF)-eome. Notably, a high proportion of the predicted ORFs are validated by mass spectrometry-based proteomics. Moreover, we identify isoforms with subcellular localization pattern in neurons. Collectively, our data advance our knowledge of RNA and protein isoform diversity in the rat brain and provide a rich resource for functional studies.
PMC	PMC6825209
PMID	31676752
DOI

Wang et al. 2019 (PRJNA526538)