ChIP-Seq experiments are used to survey interactions between protein, DNA, and RNA by combining ChIP with NGS sequencing. The technique is particularly powerful to interrogate gene regulation in many biological processes and disease states.  The most common sequencing protocol used for ChIPSeq is Single-Read 50bp (SR50), with 2-8 samples multiplexed per lane. Please refer here for more information on ChIP-Seq preparation.

Standard Results

  • Raw Data:  Demultiplexed raw read in zipped fastq format
  • Quality Control Report: Sequence data quality assessment based on FastQC package, including per-base read quality, over-represented sequences, and over-represented k-mers
  • Alignment File: Sequenced reads are aligned to a reference transcriptome to produce an aligned BAM file.

Standard Bioinformatics

  • ChIP Quality Assessment: Genome-wide peak scanning and calculation of approximate IP efficiency
  • Peak Calling: Identification of genomic regions significantly enriched for sequencing reads representing ChIP enriched sites
  • Peaks Annotation:  Annotation of peaks with nearby genes, calculation of genome-wide peak distribution and tag detection around transcription start sites
  • Motifs discovery:  Known and de novo motif scan for binding sites
  • Onotology Analysis:  Genome ontology based on peaks and gene ontology (GO) enrichment analysis of bound genes.
  • Visualization:  Processed BED format fragment file for UCSC genome browser display

Customized Bioinformatics

We can also perform customized analysis to meet specific needs of your projects.

Required Sample Input

10ng IP DNA, 10ng Input DNA