Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

GENCODE PCR-Seq Batch M1

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 M1, which is the first GENCODE validation experiment in mouse, 3148 splice junctions from GENCODE version M2 (released in December 2013) were chosen for experimental verification.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Mus musculus

SUBMITTER: Jose Gonzalez

PROVIDER: E-MTAB-3261 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

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

Dataset Information

GENCODE PCR-Seq Batch M1

Publications

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

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