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GeneiASE :
GeneiASE : Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information
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- Edsgärd, Daniel (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab
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- Iglesias, Maria Jesus (författare)
- KTH,Genteknologi,Science for Life Laboratory, SciLifeLab,Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden
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Reilly, Sarah-Jayne (författare)
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- Hamsten, Anders (författare)
- Karolinska Institutet
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- Tornvall, Per (författare)
- Karolinska Institutet
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- Odeberg, Jacob (författare)
- Karolinska Institutet,KTH,Skolan för bioteknologi (BIO),Science for Life Laboratory, SciLifeLab,Karolinska University Hospital, Sweden; Karolinska Institutet, Sweden;
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- Emanuelsson, Olof (författare)
- KTH,Skolan för bioteknologi (BIO),Science for Life Laboratory, SciLifeLab
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(creator_code:org_t)
- 2016-02-18
- 2016
- Engelska.
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Ingår i: Scientific Reports. - : Nature Publishing Group. - 2045-2322. ; 6
- Relaterad länk:
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https://doi.org/10.1...
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https://www.nature.c...
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https://urn.kb.se/re...
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https://doi.org/10.1...
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http://kipublication...
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Abstract
Ämnesord
Stäng
- Allele-specific expression (ASE) is the imbalance in transcription between maternal and paternal alleles at a locus and can be probed in single individuals using massively parallel DNA sequencing technology. Assessing ASE within a single sample provides a static picture of the ASE, but the magnitude of ASE for a given transcript may vary between different biological conditions in an individual. Such condition-dependent ASE could indicate a genetic variation with a functional role in the phenotypic difference. We investigated ASE through RNA-sequencing of primary white blood cells from eight human individuals before and after the controlled induction of an inflammatory response, and detected condition-dependent and static ASE at 211 and 13021 variants, respectively. We developed a method, GeneiASE, to detect genes exhibiting static or condition-dependent ASE in single individuals. GeneiASE performed consistently over a range of read depths and ASE effect sizes, and did not require phasing of variants to estimate haplotypes. We observed condition-dependent ASE related to the inflammatory response in 19 genes, and static ASE in 1389 genes. Allele-specific expression was confirmed by validation of variants through real-time quantitative RT-PCR, with RNA-seq and RT-PCR ASE effect-size correlations r = 0.67 and r = 0.94 for static and condition-dependent ASE, respectively.
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