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Comparison of EM-se...
Comparison of EM-seq and PBAT methylome library methods for low-input DNA
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- Han, Yanan (författare)
- Karolinska Institutet
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- Zheleznyakova, Galina Yurevna (författare)
- Karolinska Inst, Ctr Mol Med, Karolinska Univ Hosp, Dept Clin Neurosci, Stockholm, Sweden.
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- Marincevic-Zuniga, Yanara (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinska vetenskaper
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- Kakhki, Majid Pahlevan (författare)
- Karolinska Institutet
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- Raine, Amanda (författare)
- Uppsala universitet,Science for Life Laboratory, SciLifeLab,Institutionen för medicinska vetenskaper
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- Needhamsen, Maria (författare)
- Karolinska Institutet
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- Jagodic, Maja (författare)
- Karolinska Institutet
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Karolinska Institutet Karolinska Inst, Ctr Mol Med, Karolinska Univ Hosp, Dept Clin Neurosci, Stockholm, Sweden (creator_code:org_t)
- 2021-11-17
- 2022
- Engelska.
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Ingår i: Epigenetics. - : Informa UK Limited. - 1559-2294 .- 1559-2308. ; 17:10, s. 1195-1204
- Relaterad länk:
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https://doi.org/10.1...
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https://uu.diva-port... (primary) (Raw object)
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https://www.tandfonl...
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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
- DNA methylation is the most studied epigenetic mark involved in regulation of gene expression. For low input samples, a limited number of methods for quantifying DNA methylation genome-wide has been evaluated. Here, we compared a series of input DNA amounts (1-10ng) from two methylome library preparation protocols, enzymatic methyl-seq (EM-seq) and post-bisulfite adaptor tagging (PBAT) adapted from single-cell PBAT. EM-seq takes advantage of enzymatic activity while PBAT relies on conventional bisulfite conversion for detection of DNA methylation. We found that both methods accurately quantified DNA methylation genome-wide. They produced expected distribution patterns around genomic features, high C-T transition efficiency at non-CpG sites and high correlation between input amounts. However, EM-seq performed better in regard to library and sequencing quality, i.e. EM-seq produced larger insert sizes, higher alignment rates and higher library complexity with lower duplication rate compared to PBAT. Moreover, EM-seq demonstrated higher CpG coverage, better CpG site overlap and higher consistency between input series. In summary, our data suggests that EM-seq overall performed better than PBAT in whole-genome methylation quantification of low input samples.
Ämnesord
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Nyckelord
- Low input DNA
- methylome
- EM-seq
- PBAT
Publikations- och innehållstyp
- ref (ämneskategori)
- art (ämneskategori)
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