Expertise | Automation

IP Automations

SX-8G IPStar Compact epigenetic workstation
Description
SX-8G IP-Star® Compact Automated System

 

Case studies:

 

Top Five Reasons To Automate Your Epigenetic Workflow

The word "automation" may conjure up images of the future, complete with robot butlers and flying cars. The reality is that automation is here now, and it can change your everyday life significantly. In the lab, automated instruments have already impacted how researchers perform common techniques like PCR, nucleic acid purification, and Next Generation Sequencing. Today, new systems that automate the greatest hits of epigenetics research such ChIP, MeDIP, MBD capture or NGS sample prep are hitting the labs. Early adopters aren't looking back.

Get Your Epigenetics Automation On

Ok, sure -- if you haven't run a chromatin immunoprecipitation or methylated DNA immunoprecipitation assay for ages, an automated system with all the bells and whistles might not be your thing. For many scientists in the epigenetics game who are incorporating Next Generation Sequencing as their epigenome analysis method of choice, however, automation could mean the difference between getting the scoop and being the one who gets scooped.

Diagenode Product Manager, Ignacio Mazon, who provides expert support for the first epigenetics automation platforms on the market (IP-Star and IP-Star Compact), gives 5 great reasons for why you may want to hop on the epigenetics automation bandwagon.

Check them out:

  1. You need data faster: Automation means that up to 16 assays can be run simultaneously and that larger projects can be handled with ease (32 samples per day, or more than 5,000 samples per year). Whether your lab runs a single epigenetics assay repeatedly, or you need to handle multiple assays, automation will expand your lab's capabilities to get the job done quickly. With epigenetics automation, you can now spend more time with your friends.
  2. There aren't enough hours in a day: Even the most dedicated post-docs occasionally need food, rest breaks. It is a different story with automated instruments. Aside from a few minutes of some monthly upkeep, an automated instrument can be run non-stop. According to Mazon, "All it takes is about half an hour of hands on time, and then you can walk away to work on something else, instead of spending several hours at the bench." That's extra time that can be applied to critical lab activities like cracking those higher levels in Angry Birds.
  3. Variability is the enemy: We all pipet a little differently, and since many experimental procedures like ChIP and MeDIP require long, multi-step protocols, the risk of introducing variability is very high. Automated instrumentation lets you standardize your assays so that you can get consistent results from person to person, day to day, and lab to lab. "Users will also avoid issues such as cross-contamination, sample carryover, and false positives, which really pays off when you're doing something as sensitive as sequencing later on", added Mazon.
  4. Even a caveman can use it: Well, maybe not a caveman... but hung-over undergrads desk-bound PI's can certainly master it. The IP-Star Compact utilizes a slick touch screen interface to guide users every step of the way, so making protocol adjustments is as easy as creating a playlist in iTunes. Once the settings are just right, press "Start", sit back, and enjoy the show.
  5. Options are a good thing: The IP-Star Compact System has numerous uses; it's like an epigenetic Swiss Army Knife. It will easily switch between chromatin experiments and DNA methylation assays, adjust experimental conditions, try different protocol parameters, and even experiment with different reagents. Keep in mind that the assays must be magnetic bead-based. Diagenode automated systems are open platforms that provide users the flexibility to optimize conditions if needed.

IP Automation

Diagenode understands the challenges that exist when optimizing epigenetic assay conditions manually. The company has placed systems in leading cancer centers, academic institutions, and hospitals, and continues to collaborate with leading researchers in the field of epigenetics.

Diagenode systems have been used in many applications:

1. Automated immunoprecipitation of methylated DNA (MeDIP)
Automated immunoprecipitation of methylated DNA (MeDIP) using the Diagenode IP star is currently applied to several large scale cancer methylome projects some of them under the coordination of the International Cancer Genome Consortium at the Centre National de Génotypage (Evry, France). Automated MeDIP has successfully been coupled to promoter and CpG island tiling arrays as well as second generation sequencing. The automation of the immunoprecipitation has been shown to significantly increase the signal to noise ratio permitting a more rapid and reliable identification of differentially methylated candidate genes as assessed by high resolution quantitative pyrosequencing.
Dr Jörg Tost Centre National de Génotypage, Evry, France

2. Automating whole-genome DNA methylation analyses
To automate the hands-on aspect of Methylated DNA Immunoprecipitation (MeDIP) - 'Auto MeDIP' & 'Auto ChIP' - Diagenode recently introduced a robotic liquid handler. We are currently using this machine to perform a series of custom assays with qPCR, microarrays and, ultimately, Illumina Solexa 2nd-generation sequencing. The Auto MeDIP workflow qualitatively distinguishes between methylated and unmethylated fragments. Future work: we aim test the Auto MeDIP workflow with Illumina sequencing using both control DNA and, as a proof-of-principle, experimental samples. These experiments will help fine-tune the methylation-scoring algorithms for use in future studies.
Dr Stephan Beck University College London London, WC1E 6BT, United Kingdom Contact Person: Lee Butcher

3. MethylCap-sequencing (Methyl binding domain - sequencing)
DNA methylation is the most stable epigenetic mark that is strongly associated with cancer. Genome-wide mapping of DNA methylation associated with human cancers provides a readout of their cancer epigenomes. The general expection is that catalogues of the differentially methylated regions will be of high diagnostic and/or prognostic value. Most studies performed thus far have been limited to proximal promoters and CpG islands. It is possible that genomic regions outside of promoters and CpG islands are also targets for differential methylation in a 'cancer-type' specific manner. A bottleneck in the genome-wide analysis of DNA methylation has been the lack of methods amenable for genome-scale analysis. Here we present a strategy based on capturing of methylated DNA fragments using an MBD protein (MethylCap), followed by deep sequencing that allows to interrogate the entire genome. The use of automated MethylCap guarentees high reproducibility and high-throughput in generating whole-genome DNA methylation profiles of human (cancer) genomes.
Dr Henk Stunnenberg Nijmegen Center for Molecular Life Sciences Nijmegen, The Netherlands