DAP-Seq Service

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DAP-Seq Service

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CD BioSciences offers DAP-seq (DNA affinity purification sequencing) service to transfer in vivobinding experiments to in vitro, greatly improving the efficiency of DNA binding site discovery. Our service helps clients deeply understand the biological properties and binding site structure of transcription factors, which shows great value in researching the function and action mechanism of plant proteins.

DAP-Seq Protocol Overview

DAP-seq constructs transcription factor proteins binds to target genomic DNA, and enriches the bound fragments. Then, combined with high-throughput sequencing technology, sequence DNA products and analyze the data through bioinformatics methods to identify DNA binding sites of plant proteins from the whole genome. DAP can effectively address the limitations of ChIP technology in lacking target protein-specific antibodies and has broader application prospects.

DAP-Seq workflow diagram.  Figure 1. DAP-Seq workflow diagram. (O'Malley, R. C., et al., 2016)

Service Content

Service items Delivery materials and data
  • Transcription factor expression vector construction.
Plasmid lyophilized powder 2ug.
The cloned strain containing plasmid (Glycerophage) 1mL.
Vector construction COA file.
  • Cell-free expression of transcription factor proteins.
Cell-free protein expression assay report.
Western-Blot assay report.
  • DNA affinity purification.
Affinity purification lab report.
  • DAP-seq library construction.
Library construction experiment report.
  • Sequencing.
Sequencing raw data.
  • Data processing and analysis.
Bioinformatics analysis report.

Bioinformatics analysis content

  • Sequencing evaluation, including sequencing quality assessment, base composition and quality analysis, and filtering information statistics.
  • Comparison analysis, including comparison genome statistics, Reads distribution on chromosomes, sequencing depth, and saturation analysis.
  • Peak analysis, including Peak calling, Peak length distribution, Peak depth distribution, and Peak enrichment fold distribution.
  • Peak annotation, including Peak-related gene analysis, Peak distribution on gene functional elements, and GO/Pathway functional enrichment analysis of Peak-related genes.
  • Motif analysis
  • Peak merging and multi-sample clustering for each treatment group, including peak abundance calculation, PCA analysis, and correlation heat map analysis.
  • Analysis of unique peaks shared by treatment groups, including statistics of unique peaks and related genes, GO enrichment analysis, and KO enrichment analysis.
  • Analysis of peak differences between groups, including differential peak statistics, analysis of differential peak-related genes between groups, GO enrichment analysis, and KO enrichment analysis.

Notification for Sample Preparation and Handling

Sample type Details Mailing conditions
Strain and stem ≥ 1g Liquid nitrogen flash frozen, dry ice mailed.
Root ≥ 2g
Leaf and seed ≥ 3g
Fruit ≥ 5g
Inflorescence, pollen, and stamen ≥ 1g

CD BioSciences is dedicated to exploring plant proteins' regulatory mechanisms and DNA binding profiles. Our DAP-Seq protocol enables high-resolution analysis of protein-DNA interactions in plants. Please contact us if you are interested in our services. Our scientists utilize next-generation sequencing technology and cutting-edge bioinformatics analysis to provide clients with accurate and comprehensive DAP-Seq data.

References

  1. O'Malley, R. C., et al. (2016). Cistrome and Epicistrome Features Shape the Regulatory DNA Landscape. Cell. 165(5), 1280-1292.

For research use only, not for clinical use.