DAP-Seq Service (DNA affinity purification sequencing)

Comprehensive identification of TFBS (transcription factor binding sites) in whole genome-wide is essential for characterizing regulatory elements and TF function. ChIP-Seq (Chromatin immunoprecipitation sequencing) is a powerful approach for determining in vivo TFBS. However, the method is limited in scale as it depends on specific antibodies for each transcription factor, which can be technically challenging and expensive. Currently, alternatives methods DAP-Seq can offer a simple and high-throughput method to examine TF binding to its cognate target (gDNA) in a chromatin-free context, while maintaining important information related to primary genome sequence and DNA methylation. The method does not require the specific antibodies or gene-specific primers, suitable for all eukaryotes, leading to a powerful tool for understanding regulatory elements and TF function.

Advantages of DAP-Seq

• Suitable for high-throughput sample processing of entire TF ORF clone collections.
• Does not require the specific antibodies for each transcription factor, relatively cost-effective, and suitable for all eukaryotes.
• DAP-Seq retains many of the tissue/cell-line specific secondary modifications and features present in whole genome-wide.

DAP-Seq Workflow

Our highly experienced expert team executes quality management following every procedure to ensure comprehensive and accurate results. Our DAP-Seq workflow is outlined below, including library prep, protein expression, DNA affinity purification, sequencing, and bioinformatics analysis.

Figure 1. DAP-Seq workflow

Service Specifications

	Sample Requirements DNA sample: 5 µg of genomic DNA and 1 µg of Halo-ORF plasmid DNA
	Sequencing Illumina Hiseq/NovaSeq Platform ~200 bp insert size range for DNA library preparation ≥20 M clean reads
	Bioinformatics Analysis We provide customized bioinformatics analysis including: Data quality control Alignment to reference genome with mapping statistics Peak calling and annotation Differential peaks annotation Functional analysis of peak-associated genes Motif prediction Pathway analysis Visualization results

Bioinformatics workflow

Figure 2. Bioinformatics workflow of DAP-Seq

Deliverables

• The original sequencing data
• Experimental results
• Data analysis report

At CD Genomics, we provide you with high-quality sequencing and comprehensive bioinformatics analysis for your DAP-Seq project, enabling TFBS identification (transcription factor binding sites) in whole genome-wide. If you have additional requirements or questions, please feel free to contact us.

References:
[1] Ronan C. O’Malley, S. shan C. Huang, L. Song, et al. Cistrome and epicistrome features shape the regulatory DNA landscape, Cell, 165 (2016) 1280–1292.
[2] Anna Bartlett, Ronan C. O’Malley, S. shan C. Huang, et al. Mapping genome-wide transcription-factor binding sites using DAP-Seq, Nature Protocols, 12 (2017) 1659–1672.