title: Amplification of pico-scale DNA mediated by bacterial carrier DNA for small-cell-number transcription factor ChIP-seq.
abstract: BACKGROUND
  Chromatin-Immunoprecipitation coupled with deep sequencing (ChIP-seq) is used to map transcription factor occupancy and generate epigenetic profiles genome-wide. The requirement of nano-scale ChIP DNA for generation of sequencing libraries has impeded ChIP-seq on in vivo tissues of low cell numbers.
  
  
  RESULTS
  We describe a robust, simple and scalable methodology for ChIP-seq of low-abundant cell populations, verified down to 10,000 cells. By employing non-mammalian genome mapping bacterial carrier DNA during amplification, we reliably amplify down to 50 pg of ChIP DNA from transcription factor (CEBPA) and histone mark (H3K4me3) ChIP. We further demonstrate that genomic profiles are highly resilient to changes in carrier DNA to ChIP DNA ratios.
  
  
  CONCLUSIONS
  This represents a significant advance compared to existing technologies, which involve either complex steps of pre-selection for nucleosome-containing chromatin or pre-amplification of precipitated DNA, making them prone to introduce experimental biases.
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. janus.jakobsen@bric.ku.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. janus.jakobsen@bric.ku.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. janus.jakobsen@bric.ku.dk.
authors: Janus S
authors: JS
authors: Jakobsen
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. frederik@binf.ku.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. frederik@binf.ku.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. frederik@binf.ku.dk.|The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. frederik@binf.ku.dk.
authors: Frederik O
authors: FO
authors: Bagger
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. marie.sigurd@bric.ku.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. marie.sigurd@bric.ku.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. marie.sigurd@bric.ku.dk.
authors: Marie S
authors: MS
authors: Hasemann
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. mikkel.schuster@bric.ku.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. mikkel.schuster@bric.ku.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. mikkel.schuster@bric.ku.dk.
authors: Mikkel B
authors: MB
authors: Schuster
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. annekatrine.frank@bric.ku.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. annekatrine.frank@bric.ku.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. annekatrine.frank@bric.ku.dk.
authors: Anne-Katrine
authors: AK
authors: Frank
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. johannes.waage@dbac.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. johannes.waage@dbac.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. johannes.waage@dbac.dk.|The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. johannes.waage@dbac.dk.|Present address: Danish Pediatric Asthma Center, Copenhagen University Hospital Gentofte, Ledreborg Alle 34, 2820, Gentofte, Denmark. johannes.waage@dbac.dk.
authors: Johannes
authors: J
authors: Waage
authors: The Bioinformatics Centre, Department of Biology, Faculty of Natural Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. kristoffer.vittingseerup@bio.ku.dk.
authors: Kristoffer
authors: K
authors: Vitting-Seerup
authors: The Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. bo.porse@finsenlab.dk.|Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200, Copenhagen, Denmark. bo.porse@finsenlab.dk.|Danish Stem Cell Center (DanStem), Faculty of Health Sciences, University of Copenhagen, 3B Blegdamsvej, 2200, Copenhagen, Denmark. bo.porse@finsenlab.dk.
authors: Bo T
authors: BT
authors: Porse
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004269:DNA, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D021141:Nucleic Acid Amplification Techniques; D020411:Oligonucleotide Array Sequence Analysis; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000235:genetics*
chemical_list: D002843:Chromatin; D004269:DNA, Bacterial; D014157:Transcription Factors
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