ChIP Sequencing Library Preparation


Chromatin immunoprecipitation sequencing (ChIP-seq) is a method designed to examine the presence of histone modifications and transcription factors on a genome-wide scale. The general principle of ChIP-seq involves DNA-protein crosslinking, followed by fragmentation and immunoprecipitation. DNA is purified and sequenced, giving the user reads that should be enriched for sequences crosslinked to the targeted protein.

Antibody quality is an important factor that affects the outcome of ChIP-Seq experiments. The ENCODE and RoadMap consortia have guidelines for assessing antibody quality prior to ChIP-Seq. We've included some recommendations for calculating the coverage required for ChIP-Seq here: How Much Sequencing Is Required for ChIP-Seq.

There are a plethora of software solutions for ChIP-Seq data analysis including MACS, an open source solution available through Galaxy.

Genohub scientists are happy to help with complementary ChIP-Seq consultation. Contact us to describe the experiment you’re planning.


See Genohub's up-to-date list of available ChIP-Seq library prep services

ChIP-Seq Kits

Bioo Scientific NEXTflex ChIP-Seq Kit

The NEXTflex Illumina compatible ChIP-Seq Kit was the first commercially available kit designed specifically for the construction of libraries from chromatin immunoprecipitated (IP’d) DNA. The kit allows users to start from a low as 1 ng of starting material and enables the determination and abundance of protein bound DNA targets across the genome. The kit is compatible with up to 192 available single or dual indexed barcodes.

Protocol Overview:

  1. End-repair
  2. Adenylation
  3. Barcoded adapter ligation
  4. PCR Amplification
  5. Quantification

Diagenode idEAL ChIP

The idEAL ChIP kit is designed for chromatin immunoprecipitation prior to library preparation.

Protocol Overview:

  1. Collect suspension or adherent cells
  2. Chromatin preparation
  3. Bioruptor ® used for chromatin shearing
  4. DNA purification
  5. Library Prep

Illumina TruSeq Chip

The TruSeq Chip Kit has been designed for ChIP-Seq (chromatin immunoprecipitation sequencing) applications which allow for the determination and abundance of DNA bound targets of interest across the genome. Protein - DNA interactions regulate gene expression and ChIP-Seq has become the most widely adapted way for identifying the binding sites across a broad range of targets. Users can start with as little as 5 ng of DNA and multiplex up to 12 samples with a single kit (24 adapter barcode available in total).

Protocol Overview:

  1. Quantification of input DNA
  2. End-repair
  3. A-tailing
  4. Ligation of barcoded adapters
  5. Purification of ligated products
  6. PCR amplification
  7. Library validation