Transcriptomics

Dataset Information

709

Transcription profiling by high throughput sequencing of mouse brain, heart, kidney, liver, lung, skeletal muscle organ, spleen and testis

ABSTRACT: As part of the ENCODE consortium the GENCODE project is producing a reference gene set through manual and automated gene prediction. Selected transcript models are verified experimentally by RT-PCR amplification of at least one of their unique splice junctions followed by high-throughput sequencing. The experiment targets are manually annotated transcripts with novel or putative status, non-pseudogene biotype and unique splice junctions which have not been validated previously and are not supported by mouse RNAseq data from the ENCODE project. In Batch M2, 808 splice junctions from GENCODE version M4 (released in December 2014) were chosen for experimental verification.

REANALYSED by: E-MTAB-4644

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus  

SUBMITTER: Jen Harrow   Anne-Maud Ferreira   Jose M Gonzalez   Roderic Guigo   Alexandre Reymond  

PROVIDER: E-MTAB-4644 | ArrayExpress | 2016-04-28

SECONDARY ACCESSION(S): ERP015150

REPOSITORIES: ArrayExpress, ENA

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Publications

Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine perce  ...[more]

PMID: 22955982

Publication: 1/2

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