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