Transcriptomics

Dataset Information

301

Sequencing Universal Human Reference RNA by Smart-seq and early barcoding library preparation methods


ABSTRACT: Many library preparation methods are available for gene expression quantification. Here, we sequenced and analysed Universal Human Reference RNA (UHRR) prepared using Smart-Seq2, TruSeq (public data) and a protocol using unique molecular identifiers (UMIs) that all include the ERCC spike-in mRNAs to investigate the effects of amplification bias on expression quantification. UHRR 10 and 12 replicates for Smart-seq2 and UMI-seq library preparation methods, respectively.

ORGANISM(S): Homo sapiens  

SUBMITTER: Ines Hellmann   Swati Parekh 

PROVIDER: E-GEOD-75823 | ArrayExpress | 2016-05-13

SECONDARY ACCESSION(S): GSE75823SRP067154PRJNA305438

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

The impact of amplification on differential expression analyses by RNA-seq.

Parekh Swati S   Ziegenhain Christoph C   Vieth Beate B   Enard Wolfgang W   Hellmann Ines I  

Scientific reports 20160509


Currently, quantitative RNA-seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this affects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined by their mapping position, which does not distinguish  ...[more]

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