Transcriptomics

Dataset Information

591

Transcription profiling by high throughput sequencing of polyA+ RNAs from eight different human tissues to test a set of de novo transcript models (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.

OTHER RELATED OMICS DATASETS IN: E-MTAB-4644

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens  

SUBMITTER: Tim Hubbard   Jose M Gonzalez   Roderic Guigo   Alexandre Reymond  

PROVIDER: E-MTAB-1309 | ArrayExpress | 2012-10-01

SECONDARY ACCESSION(S): ERP001850

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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