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Method Article
RELACS: a novel in-nuclei barcoding strategy for high-throughput ChIP-seq
Laura Arrigoni
Deep Sequencing Facility, Max Planck Institute of immunobiology and epigenetics, Freiburg
Corresponding Author
Ulrike Boenisch
Deep Sequencing Facility, Max Planck Institute of immunobiology and epigenetics, Freiburg
Corresponding Author
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Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is a widely used technique to study the genome-wide distribution of chromatin-associated proteins. Despite many improvements, ChIP-seq still remains a labor-intense process for which sample preparation (chromatin extraction, fragmentation, immunoprecipitation and library preparation) is performed individually for each sample. Here we present a novel in-nuclei chromatin barcoding strategy for high-throughput ChIP-seq. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ) relies on intra-nuclear chromatin fragmentation using restriction enzymes and ligation of DNA barcodes to chromatin. Nuclei labelled with different barcodes are pooled for combined ChIP ensuring maximal data comparability and throughput. RELACS has been designed as a broadly applicable method for fixed cells extracted from any tissues, and demonstrated on active and repressive histone modifications as well as transcription factors.
Keywords
ChIP-seq, high-throughput, molecular barcoding, nuclei extraction, low cell ChIP, quantitative analysis, automation
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RELACS barcodes Sequences of RELACS barcodes
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Method Article
RELACS: a novel in-nuclei barcoding strategy for high-throughput ChIP-seq
Laura Arrigoni
Deep Sequencing Facility, Max Planck Institute of immunobiology and epigenetics, Freiburg
Corresponding Author
Ulrike Boenisch
Deep Sequencing Facility, Max Planck Institute of immunobiology and epigenetics, Freiburg
Corresponding Author
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
History
CURRENT STATUS: Posted
Version 1
Posted 22 Aug, 2018
No community comments so far
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is a widely used technique to study the genome-wide distribution of chromatin-associated proteins. Despite many improvements, ChIP-seq still remains a labor-intense process for which sample preparation (chromatin extraction, fragmentation, immunoprecipitation and library preparation) is performed individually for each sample. Here we present a novel in-nuclei chromatin barcoding strategy for high-throughput ChIP-seq. The method, called RELACS (Restriction Enzyme-based Labeling of Chromatin in Situ) relies on intra-nuclear chromatin fragmentation using restriction enzymes and ligation of DNA barcodes to chromatin. Nuclei labelled with different barcodes are pooled for combined ChIP ensuring maximal data comparability and throughput. RELACS has been designed as a broadly applicable method for fixed cells extracted from any tissues, and demonstrated on active and repressive histone modifications as well as transcription factors.
Figure 1
Figure 2
Figure 3