title: A comparative study of ChIP-seq sequencing library preparation methods.
abstract: ChIP-seq is the primary technique used to investigate genome-wide protein-DNA interactions. As part of this procedure, immunoprecipitated DNA must undergo "library preparation" to enable subsequent high-throughput sequencing. To facilitate the analysis of biopsy samples and rare cell populations, there has been a recent proliferation of methods allowing sequencing library preparation from low-input DNA amounts. However, little information exists on the relative merits, performance, comparability and biases inherent to these procedures. Notably, recently developed single-cell ChIP procedures employing microfluidics must also employ library preparation reagents to allow downstream sequencing.
  
  
  
  In this study, seven methods designed for low-input DNA/ChIP-seq sample preparation (Accel-NGS® 2S, Bowman-method, HTML-PCR, SeqPlex™, DNA SMART™, TELP and ThruPLEX®) were performed on five replicates of 1 ng and 0.1 ng input H3K4me3 ChIP material, and compared to a "gold standard" reference PCR-free dataset. The performance of each method was examined for the prevalence of unmappable reads, amplification-derived duplicate reads, reproducibility, and for the sensitivity and specificity of peak calling.
  
  
  
  We identified consistent high performance in a subset of the tested reagents, which should aid researchers in choosing the most appropriate reagents for their studies. Furthermore, we expect this work to drive future advances by identifying and encouraging use of the most promising methods and reagents. The results may also aid judgements on how comparable are existing datasets that have been prepared with different sample library preparation reagents.
authors: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
authors: Arvind Y M
authors: AY
authors: Sundaram
authors: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
authors: Timothy
authors: T
authors: Hughes
authors: Zymo Research Corp., 7062 Murphy Ave., Irvine, CA, 92614, USA.
authors: Shea
authors: S
authors: Biondi
authors: Takara Bio USA, Inc., 1290 Terra Bella Avenue, Mountain View, 94043, CA, USA.
authors: Nathalie
authors: N
authors: Bolduc
authors: Mass. General Hospital, Mol. Biol., Harvard Medical School, 185 Cambridge St, CPZN 7250, Boston, 02114, MA, USA.|Present address: Directed Genomics, 240 County Road, Ipswich, MA, 01938, USA.
authors: Sarah K
authors: SK
authors: Bowman
authors: Department Molecular Biology & Microbiology and Howard Hughes Medical Institute, Tufts University, 136 Harrison Avenue, Boston, 02111, MA, USA.
authors: Andrew
authors: A
authors: Camilli
authors: Zymo Research Corp., 7062 Murphy Ave., Irvine, CA, 92614, USA.
authors: Yap C
authors: YC
authors: Chew
authors: Swift Biosciences, Inc., Suite 100, 58 Parkland Plaza, Ann Arbor, 48103, MI, USA.
authors: Catherine
authors: C
authors: Couture
authors: Takara Bio USA, Inc., 1290 Terra Bella Avenue, Mountain View, 94043, CA, USA.
authors: Andrew
authors: A
authors: Farmer
authors: Rubicon Genomics, Inc., 4743 Venture Drive, Ann Arbor, 48108, MI, USA.
authors: John P
authors: JP
authors: Jerome
authors: Department Molecular Biology & Microbiology and Howard Hughes Medical Institute, Tufts University, 136 Harrison Avenue, Boston, 02111, MA, USA.
authors: David W
authors: DW
authors: Lazinski
authors: Swift Biosciences, Inc., Suite 100, 58 Parkland Plaza, Ann Arbor, 48103, MI, USA.
authors: Andrew
authors: A
authors: McUsic
authors: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 117609, Singapore, Republic of Singapore.
authors: Xu
authors: X
authors: Peng
authors: Rubicon Genomics, Inc., 4743 Venture Drive, Ann Arbor, 48108, MI, USA.
authors: Kamran
authors: K
authors: Shazand
authors: Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), 117609, Singapore, Republic of Singapore.
authors: Feng
authors: F
authors: Xu
authors: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway. robert.lyle@medisin.uio.no.
authors: Robert
authors: R
authors: Lyle
authors: Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway. gregor.gilfillan@medisin.uio.no.
authors: Gregor D
authors: GD
authors: Gilfillan
mesh_terms: D047369:Chromatin Immunoprecipitation / Q000379:methods; D002874:Chromosome Mapping; D015723:Gene Library; D016678:Genome; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D006801:Humans; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
keywords: Chromatin immunoprecipitation; HTS; Low-input; Micro-ChIP; NGS