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lobChIP: from cells to sequencing ready ChIP libraries in a single day
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab.
Uppsala University, Science for Life Laboratory, SciLifeLab.
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2015 (English)In: Epigenetics & Chromatin, ISSN 1756-8935, E-ISSN 1756-8935, Vol. 8, 25Article in journal (Refereed) Published
Abstract [en]

Background: ChIP-seq is the method of choice for genome-wide studies of protein-DNA interactions. We describe a new method for ChIP-seq sample preparation, termed lobChIP, where the library reactions are performed on crosslinked ChIP fragments captured on beads. Results: The lobChIP method was found both to reduce time and cost and to simplify the processing of many samples in parallel. lobChIP has an early incorporation of barcoded sequencing adaptors that minimizes the risk of sample cross-contamination and can lead to reduced amount of adaptor dimers in the sequencing libraries, while allowing for direct decross-linking and amplification of the sample. Conclusions: With results for histone modifications and transcription factors, we show that lobChIP performs equal to or better than standard protocols and that it makes it possible to go from cells to sequencing ready libraries within a single day.

Place, publisher, year, edition, pages
2015. Vol. 8, 25
Keyword [en]
ChIP-seq, Chromatin immunoprecipitation, Illumina, NGS, Library preparation
National Category
Medical Genetics
Identifiers
URN: urn:nbn:se:uu:diva-260287DOI: 10.1186/s13072-015-0017-5ISI: 000358203100001PubMedID: 26195988OAI: oai:DiVA.org:uu-260287DiVA: diva2:847748
Funder
Swedish Research Council, B0605201Swedish Research Council, A0350501
Available from: 2015-08-21 Created: 2015-08-18 Last updated: 2017-12-04Bibliographically approved

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Wallerman, OlaWadelius, Claes
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