Wang et al. 2019 (PRJNA526538)

General Details

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

Study Links

Repository Details

SRA SRP188139
ENA SRP188139
GEO
BioProject PRJNA526538

Publication

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
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR8711056 PRJNA526538 Rattus norvegicus Ribo-Seq
SRR8711057 PRJNA526538 Rattus norvegicus Ribo-Seq
SRR8711058 PRJNA526538 Rattus norvegicus Ribo-Seq
SRR8711059 PRJNA526538 Rattus norvegicus Ribo-Seq
SRR8711060 PRJNA526538 Rattus norvegicus Ribo-Seq
SRR8711061 PRJNA526538 Rattus norvegicus Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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