ChIP-Seq combines chromatin immunoprecipitation (ChIP) assays with sequencing, and is a powerful method for identifying genome-wide DNA binding sites for transcription factors and other proteins. This method can reveal insights into gene regulation events that play a role in various diseases and biological pathways, such as development and cancer progression. ChIP-Seq enables thorough examination of the interactions between proteins and nucleic acids on a genome-wide scale.

Our standard service includes alignment of short reads to an appropriate genome, data quality control and normalization, peak calling and visualization, as well as motif discovery.

  • Quality control of raw sequencing reads
  • Alignment to standard reference genome and mapping to appropriate gene annotations
  • Gene-level abundance measurements
  • Data normalization (read depth and transcript length)
  • Sample-to-sample quality assessment via unsupervised hierarchical clustering principle component analysis
  • Determination of sample outliers and/or batch effects, as well as downstream strategy
  • Differential expression testing for sample pairs (condition A vs condition B)

Extended services are available, which supplement our standard/fixed workflow described above:

  • Acquiring data from 3rd party services, such as ArrayExpress or GEO
  • Iterative customization of results and plots for presentations, publications, grants, etc...
  • Batch correction and modeling
  • Integration with other data

Service info

  • Category:Bioinformatics
  • Skills:R, TF/biology, statistics
  • Inquire: Email us