Dataset Information

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

ABSTRACT: Transcriptome of HEK and B cells were analyzed by microarray and RNA-Seq parallely. Both platforms were then compared in terms of sensitivity. To assess whether values were a reliable indicator of gene activity, we correlated these values with hypophosphorylated RNA polymerase II (PolIIa) occupancy, used as a landmark of transcription initiation. For HEK, we identified PolIIa islands by chromatin immunoprecipitation and sequencing (ChIP-Seq). Overall design: For HEK and B cell, samples were hybridized as biological and technical duplicates on Illumina HumanRef8 V2.0 BeadChips. PolIIa Chip-Seq performed on HEK.

INSTRUMENT(S): Illumina humanRef-8 v2.0 expression beadchip

SUBMITTER: Marc Sultan

PROVIDER: GSE11892 | GEO | 2008-07-03

SECONDARY ACCESSION(S): PRJNA105719

REPOSITORIES: GEO

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Publications

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

Sultan Marc M Schulz Marcel H MH Richard Hugues H Magen Alon A Klingenhoff Andreas A Scherf Matthias M Seifert Martin M Borodina Tatjana T Soldatov Aleksey A Parkhomchuk Dmitri D Schmidt Dominic D O'Keeffe Sean S Haas Stefan S Vingron Martin M Lehrach Hans H Yaspo Marie-Laure ML

Science (New York, N.Y.) 20080703 5891

The functional complexity of the human transcriptome is not yet fully elucidated. We report a high-throughput sequence of the human transcriptome from a human embryonic kidney and a B cell line. We used shotgun sequencing of transcripts to generate randomly distributed reads. Of these, 50% mapped to unique genomic locations, of which 80% corresponded to known exons. We found that 66% of the polyadenylated transcriptome mapped to known genes and 34% to nonannotated genomic regions. On the basis o ...[more]

PMID: 18599741

Dataset Information

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

Publications

A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome.

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