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GENCODE PCR-Seq Batch IX

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 followed by sequencing. In batch IX, a set of de novo transcript models was tested aiming to incorporate new long non-coding RNA models into the GENCODE annotation. The original set was built with Cufflinks from ENCODE RNAseq data derived from 15 cell lines by the Gingeras (CSHL) and Wold (CalTech) labs. A subset of multiexonic transcripts not overlapping the GENCODE v10 annotation was selected for this experiment.

ORGANISM(S): Homo sapiens

SUBMITTER: Jose Gonzalez

PROVIDER: E-MTAB-1309 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome.

Howald Cédric C Tanzer Andrea A Chrast Jacqueline J Kokocinski Felix F Derrien Thomas T Walters Nathalie N Gonzalez Jose M JM Frankish Adam A Aken Bronwen L BL Hourlier Thibaut T Vogel Jan-Hinnerk JH White Simon S Searle Stephen S Harrow Jennifer J Hubbard Tim J TJ Guigó Roderic R Reymond Alexandre A

Genome research 20120901 9

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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