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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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE75823 | GEO | 2016/05/13

SECONDARY ACCESSION(S): PRJNA305438

REPOSITORIES: GEO

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

Project description: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.

2016-05-13 | E-GEOD-75823 | biostudies-arrayexpress

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Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls

Project description:Microarray coverage of UHRR was determined by counting the number of spots with intensities exceeding the 1% and 5% false positive rates defined using the yeast negative control spots. Seven microarrays from different print runs were used. In four experiments, the UHRR was labeled with Cy5 and in three experiments with Cy3. Labeled UHRR was co-hybridized with Common Reference RNA (CRF) developed at Stanford University (8) labeled with the alternate dye. A reference experiment design type is where all samples are compared to a common reference. Keywords: reference_design

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Microarray Coverage of Universal Human Reference RNA on microarrays with yeast controls

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Counting and correcting errors within unique molecular identifiers to generate absolute numbers of sequencing molecules [scRNA-Seq]

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