Chip Sequencing

Types of Libraries:

1. Chip Sequencing
2. Medip Sequencing
3. RRBS (Reduced Representation Bisulfite)
4. Whole genome (or Oxy) Bisulfite Sequencing

Chromatin immunoprecipitation, or ChIP, is established in epigenetic research as a powerful method for investigating genome-wide DNA-protein interactions in the cell, aiding researchers in understanding chromatin dynamics and epigenetic mechanisms. With the recent technological advancement of next generation sequencing, the ChIP assay can be combined with the power of massively parallel sequencing platforms like Illumina to map the exact binding sites across the entire genome to which the protein of interest is bound.

Some common targets for ChIP-seq:

• Transcription factors
• Histone methylation
• Histone acetylation
• Histone ubiquitination

Sequencing using HiSEQ 2500
Paired End 150 base Read length
40 Million Paired-end Reads
Standard Bioinformatics Included

Standard Chip Seq Bioinformatics:
Quality Control

1. Raw data QC.
2. Removal of low quality reads and trimming of Low quality bases.
3. Adaptor trimming.

Chip Seq Analysis:

1. Mapping of Filtered data to reference.
2. Peak Detection.
3. Nucleosome Positioning.
4. Differential peak callign between samples.
5. Gene Target/ Motif identifications.
6. Gene Ontology & Pathway Analysis