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ChIP Sequencing

ChIP-seq is a genomics technology developed to map binding sites of a DNA-interacting protein across the genome. Examples of DNA-interacting proteins include transcription factors, histones, and enzymes for DNA repair and modification. A common application of ChIP-seq is to locate transcription factor binding patterns under different conditions, such as development stages or pathological conditions.

ChIP-seq starts with covalent cross-linking of DNA with interacting proteins, then shearing of chromatin into fragments, followed by enrichment of the protein of interest with its bound DNA by immunoprecipitation using an antibody specific for the protein. Subsequently, after dissociating the enriched protein-DNA complex, the released DNA fragments are subjected to sequencing. One key experimental factor in the ChIP-Seq process is the quality of the antibody used in the enrichment step, as the use of a poor-quality antibody can lead to high experimental noise due to non-specific precipitation of DNA fragments.

NUSeq accepts ChIP DNA, as well as input DNA, for sequencing library construction and then sequencing. Please see below for sample submission guidelines.

ChIP-seq Library Prep Pricing

Library prep costs are listed on the Core Pricing page.


ChIP Sequencing

 Sequencing Mode

A single-end 75 bp run is sufficient for most cases. Use of paired-end and/or longer reads may help reads alignment, especially to repetitive regions. For run cost of the different sequencing options, please check our pricing structure.

 Service Request

If needed, project consultation is provided free-of-charge. ChIP-seq services can be requested through NUcore. Please finish and submit our project intake form when requesting service.

 Sample Submission

For library prep, 10 ng of ChIP and input DNA is required. For DNA quantification, fluorometric-based methods, such as Qubit or PicoGreen, are preferred. Spectrophotometric-based methods, such as Nanodrop, may not be accurate.


Data analysis is provided upon request. Standard ChIP-seq bioinformatics service includes sequencing data QC, alignment and peak calling. Learn more about bioinformatics services.

 Data Storage Policy

ChIP-seq data is stored on the NUSeq server space for one year from the date of generation. It is recommended to transfer data files to the user's own space after they are generated.

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