August 23, 2017
This year we are celebrating the 10 year anniversary of the invention of ChIP-Seq. This technique has come a long way since it was first published in 2007. An infographic charting the history of ChIP-Seq is available in our guide to bioinformatics blog post.
Before joining elucidaid, as postdocs at the NIH, we optimized and performed hundreds of ChIP-Seq experiments. Although not a comprehensive list, here is a summary review of our most favorite suppliers and service providers in this niche:
NOTE: We are not affiliated or connected to any of the companies mentioned below, in any shape or form. This is not an endorsement of their products or services.
The leader in next-generation sequencing technologies, Illumina began its journey towards dominating the next-generation sequencing market in 2007, when it acquired Solexa, Inc. In 2011, it introduced the MiSeq System for small whole-genome sequencing (e.g. bacteria and yeast genomes), amplicon sequencing, gene expression profiling, small RNA analysis. We highly recommend you check out their website to learn more about techniques, protocols and more.
Figure. Illumina website contains a wealth of useful information (guides, tips, and resources)
A major supplier of top quality antibodies, Abcam has an interesting history which you can read here: http://www.abcam.com/index.html?pageconfig=story
Their antibodies are verified for different techniques, and their website provides a lot of useful information and protocols. Abcam was always the first port of call for us when looking to use a new antibody.
3- Clontech (Takara)
Provider of innovative kits and reagents that can make life super easy for those performing challenging ChIP-Seq experiments. Although Illumina provides standard kits for their sequencing platforms, on numerous occasions, we've had to resort to Clontech material to successfully complete a challenging ChIP-Seq experiment. For example, we had great success with their library preparation kits for low-input DNA templates.
4- Active Motif
A rapidly growing company that provides a number of solutions related to ChIP-Seq. If your area of study is in the epigenetics or related fields, we recommend you check out their website or talk to their representatives at conferences and meetings.
Although they are well known for their enzymes (PCR and restriction enzymes), they also provide reagents and kits for ChIP-Seq library prep. We have had great success using the NEBNext library quant kit for Illumina, to ensure our library preps were of high quality.
A superb service provider for performing next-generation sequencing. Based in New Jersey, USA, they have excellent customer service and fast turn around. They are an Illumina-approved service provider (see the post on bioinformatics for more details). We always had good experience with them.
We remember the day when one of our most important and time-sensitive ChIP-seq experiments was salvaged when someone recommended that we use the S220 Focused-ultrasonicator for shearing DNA samples. Not only beautifully consistent and within-range DNA fragments were produced, the efficiency of our immunoprecipitations increased dramatically. Lower generated heat and reduced sonication times did not alter the epitopes as severely as traditional sonication methods (e.g. probe or water bath sonication). If you are starting out or performing many ChIP-Seq or RNA-Seq experiments, we highly recommend giving this system a try. We had good experience with their customer service on the phone and in person.
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