Transcriptomics

Dataset Information

637

GENCODE PCR-Seq Batch XVII


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 (RT-PCR-seq). The experimental 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 RNAseq data from the ENCODE and GTEx projects. For Batch XVII, 1159 splice junctions which failed this experimental verification in previous experiments were tested again. On this occasion, newly designed PCR primers were used and compared with the original ones. In addition, the original tissue panel was widened with the inclusion of eight new tissues.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens  

SUBMITTER: Anne-Maud Ferreira   Jose M Gonzalez   Roderic Guigo   Jacqueline Chrast   Alexandre Reymond   Adam Frankish  

PROVIDER: E-MTAB-5527 | ArrayExpress | 2017-03-31

SECONDARY ACCESSION(S): ERP021745

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]

Publication: 1/2

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