A method for generating highly multiplexed ChIP-seq libraries

BackgroundThe barcoding of next generation sequencing libraries has become an essential part of the experimental design. Barcoding not only allows the sequencing of more than one sample per lane, but also reduces technical bias. However, current barcoding strategies impose significant limitations and/or technical barriers in their implementation for ChIP-sequencing.FindingsConverting Y-shaped sequencing adapters to double stranded DNA prior to agarose gel size selection reduces adapter dimer contamination and quantitating the number of cycles required for amplification of the library with qPCR prior to library amplification eliminates library over-amplification.ConclusionsWe describe an efficient and cost effective method for making barcoded ChIP-seq libraries for sequencing on the Illumina platform.

• Publication year

  2014

• Venue

  BMC Research Notes

• Publication date

  2014-05-22

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1186/1756-0500-7-312PMID 24885602PMCID 4048252
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A method for generating highly multiplexed ChIP-seq libraries

  2014cited by this paper
• Protein engineering: making ubiquitin specific.

  2013cited by this paper
• A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

  2011cited by this paper
• Large Scale Loss of Data in Low-Diversity Illumina Sequencing Libraries Can Be Recovered by Deferred Cluster Calling

  2011cited by this paper
• Optimal enzymes for amplifying sequencing libraries

  2011cited by this paper
• The histone variant macroH2A1 marks repressed autosomal chromatin, but protects a subset of its target genes from silencing.

  2010cited by this paper
• The conserved Lysine69 residue plays a catalytic role in Mycobacterium tuberculosis shikimate dehydrogenase

  2009cited by this paper
• ChIP–seq: advantages and challenges of a maturing technology

  2009cited by this paper
• BMC Genomics BioMed Central Methodology article

  2008cited by this paper
• IDENTIFICATION OF GENETIC VARIANTS USING BARCODED MULTIPLEXED SEQUENCING

  2008cited by this paper
• Model-based Analysis of ChIP-Seq (MACS)

  2008cited by this paper
• Splicing regulates NAD metabolite binding to histone macroH2A

  2005cited by this paper
• Developmental and tissue expression patterns of histone macroH2A1 subtypes

  1997cited by this paper
• DNA rehybridization during PCR: the 'Cot effect' and its consequences.

  1996cited by this paper

• An evolutionarily conserved constellation of functional cis-elements programs the virus-responsive fate of the human (epi)genome

  2025cites this paper
• The sex-biased chromatin modifier SMC1A promotes autoimmunity by shaping inflammatory pathways in patients with SLE

  2025influential citation
• H3K56 acetylation affects Candida albicans morphology and secreted soluble factors interacting with the host.

  2024cites this paper
• Combinatorial targeting of a specific EMT/MET network by macroH2A variants safeguards mesenchymal identity

  2023influential citation
• Structural Basis of Dual Specificity of Sinorhizobium meliloti Clr, a cAMP and cGMP Receptor Protein

  2023cites this paper
• Structural basis of bifunctionality of Sinorhizobium meliloti Clr, a cAMP and cGMP receptor protein

  2022cites this paper
• Repurposing the lineage-determining transcription factor Atoh1 without redistributing its genomic binding sites

  2022cites this paper
• Effects of Hst3p inhibition in Candida albicans: a genome-wide H3K56 acetylation analysis

  2022cites this paper
• Typical Enhancers, Super-Enhancers, and Cancers

  2022cites this paper
• The TΑp63/BCL2 axis represents a novel mechanism of clinical aggressiveness in chronic lymphocytic leukemia

  2022cites this paper
• A recurrent chromosomal inversion suffices for driving escape from oncogene-induced senescence via subTAD reorganization.

  2021cites this paper
• Nhp2 is a reader of H2AQ105me and part of a network integrating metabolism with rRNA synthesis

  2021cites this paper
• Analysis of the Chromosomal Localization of Yeast SMC Complexes by Chromatin Immunoprecipitation.

  2020cites this paper
• Genomic instability is an early event driving chromatin reorganization and escape from oncogene-induced senescence

  2020cites this paper
• Identification of a dynamic gene regulatory network required for pluripotency factor‐induced reprogramming of mouse fibroblasts and hepatocytes

  2020cites this paper
• Atoh1 is repurposed from neuronal to hair cell determinant by Gfi1 acting as a coactivator without redistributing Atoh1’s genomic binding sites

  2019cites this paper
• The lysine‐specific methyltransferase KMT2C/MLL3 regulates DNA repair components in cancer

  2019cites this paper
• GemC1 governs multiciliogenesis through direct interaction with and transcriptional regulation of p73

  2019cites this paper
• Protein Is a Critic al Component of GPR 158 / OCN Signaling and Ameliorates Age-Related Memory Loss Graphical Abstract Highlights

  2018cites this paper
• RbAp48 Protein Is a Critical Component of GPR158/OCN Signaling and Ameliorates Age-Related Memory Loss

  2018cites this paper
• Tripartite Chromatin Localization of Budding Yeast Shugoshin Involves Higher-Ordered Architecture of Mitotic Chromosomes

  2018cites this paper
• The Histone Variant MacroH2A Blocks Cellular Reprogramming by Inhibiting Mesenchymal-to-Epithelial Transition

  2018cites this paper
• Genome-wide analysis of chromatin structures in Trypanosoma brucei using high-resolution MNase-ChIP-seq.

  2017cites this paper
• Genome-wide studies reveal novel and distinct biological pathways regulated by SIN3 isoforms

  2016cites this paper
• The dual role of LSD1 and HDAC3 in STAT5-dependent transcription is determined by protein interactions, binding affinities, motifs and genomic positions

  2016cites this paper
• Using RNA-seq for Analysis of Differential Gene Expression in Fungal Species.

  2016cites this paper
• Composite macroH2A/NRF-1 Nucleosomes Suppress Noise and Generate Robustness in Gene Expression.

  2015cites this paper
• Next Generation Sequencing and Microbiome Evaluation: Molecular Microbiology and Its Impact on Human Health

  2015cites this paper
• Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

  2015cites this paper
• Genome-wide errant targeting by Hairy

  2015cites this paper
• Ets homologous factor regulates pathways controlling response to injury in airway epithelial cells

  2014cites this paper