Bioruptor® Pico sonication device for RNA,Chromatin and DNA shearing for Next-Generation-Sequencing

Follow our guidelines and find the good parameters for your expected DNA size: DNA shearing with the Bioruptor® Pico

Neonatal screening cards provide a valuable bio-bank for retrospective studies. We have used the Bioruptor Pico and IP-Star Compact instrument along with the Auto MeDIP and IPure v2 kit to generate genome-wide DNA methylation profiles using only minute DNA inputs. Using the Diagenode instruments and products has generated reproducible results and saved us hands-on time. We are satisfied with the level of service and technical support and would recommend Diagenode to all others working in the field of epigenetics.

Read the full abstract for Genome-wide DNA methylation profiling with MeDIP-seq using archived dried blood spots
Dr. Nicklas Heine Staunstrup, Faculty of Health, Institute of Biomedicine, Aarhus University, Denmark

I work with Diagenode’s Plant ChIP-seq kit and shear the DNA on the Bioruptor Pico for the last year and I have to say that these two products saved my PhD project! Some time ago, our well-established ChIP protocol suddenly stopped to work and after long time of figuring out the reason, we invested into Bioruptor Pico. I am very satisfied from the way it works, plus it’s super quiet! Combining the sonicator with the Plant ChIP-seq kit we finally got things working. I have also decided to try the Microplex Library Prep kit, which is amazing. I have been working with other kits and I find this one efficient and very easy to use. Recently, I have tested one of the epigenetics antibody (H3K4me3) and it works very well on the plant tissue, together with the ChIP-seq kit and Bioruptor.

Thanks Diagenode for saving my PhD!
Kamila Kwasniewska, Plant Developmental Genetics, Smurfit Institute, Trinity College, Dublin

I have extensively used the antibodies against the histone modifications H3K4me3, H3k27me3, H3K9ac, H4k8ac and H3K18ac provided by Diagenode. The high level of specificity and selectivity of these antibodies in mouse brain samples, confirmed by using several negative and positive controls run in parallel with mouse brain tissue samples, ensured successful and reproducible results. I have been a Diagenode costumer for over one year now and I am extremely satisfied with the efficiency of the Bioruptor Pico for chromatin shearing as well as all of the ChIP materials (i.e., antibodies, blocking peptides, primer pairs for qPCR) provided by this company. Many thanks.
Dr. Ermelinda Lomazzo, Institute of Physiological Chemistry, AG Prof. Beat Lutz. University Medical Center of the Johannes Gutenberg University Mainz, Germany

We are particularly satisfied with the Bioruptor^® Pico that we have recently purchased. Since we have started using this novel machine, all experiments for our epignetics research have been much more easy to perform. This machine is really a great thing for us. The whole department has now started using this novel device.
Dr. Marco Pontoglio, Head of the Team "Expression Génique, Développement et Maladies" (EGDM) and Director of the “Development, Cancer and Reproduction”, Department Institut Cochin, Université Paris-Descartes

Diagenode has provided a Bioruptor^® Pico demo instrument to us for 2 weeks in September. We were getting very reproducible results between different tubes in the same sonication as well as between replicate experiments. We have obtained considerably improved results especially for cross-linked chromatin from mammalian cells that has always been a problem for us with the old Bioruptor. A bonus also was a reduced sonication time, although the preparation time is slightly delayed due to the glutinous nature of the beads.
Dr. Tatyana Nesterova, Department of Biochemistry, University of Oxford

The new Bioruptor^® Pico machine has reduced the amount of time spent sonicating Chromatin by a massive amount. Some protocols require quite harsh fixing conditions which meant fragmenting DNA on the old machine was taking many rounds and several times. With the new Bioruptor^® Pico machine these sonications were taking just one round of 10 cycles thereby reducing the fragmentation time substantially. Following sonication, I have used the new IDeal ChIP-seq kit. This is a nice straight forward kit that if followed with an appropriate chip validated antibody gave amazing chip-seq results that worked time and again with several different transcription factors. I would recommend both kits for good, consistant chromatin work.
Dr. Karen Dawson, RNA Biology Group, Cancer Research UK Manchester Institute at the University of Manchester

The Bioruptor® NGS* is a robust user-friendly sonication system that is key for both reproducible chromatin shearing and DNA shearing. The Bioruptor® NGS consistently delivered optimal DNA shearing that was critical in generating homogeneous sequencing libraries for our experiments. We also observed excellent chromatin shearing result that were crucial for our epigenetic mapping projects.
Dr. Sascha Tierling, Department of Genetics and Epigenetics, Prof . Dr. Jörn Walter's lab, Universität des Saarlandes, Germany.

Protocols

Chromatin shearing - Guide for successful chromatin preparation using the Bioruptor^® Pico Chromatin immunoprecipitation (ChIP) is a common tool used to study protein-DNA interactions in c...	Download
Chromatin shearing from tissue protocol using Diagenode’s Chromatin shearing optimization kit - Low SDS and Bioruptor^® Standard, Plus or Pico This protocol describes the chromatin preparation from fresh or frozen tissues. The isolated chro...	Download
Chromatin shearing with the Bioruptor Pico 10 µl - 300 µl HeLa cells are fixed with 1% molecular grade formaldehyde (for 8 min at room temperature). Nucleu...	Download
Chromatin shearing with the Bioruptor^® Pico 500 µl - 2 ml Chromatin shearing from HeLa cells is performed according to Diagenode’s Chromatin Shearing...	Download
Chromatin shearing with the Bioruptor® Pico, 0.2 ml Bioruptor® Microtubes and the corresponding holder The first critical step of a successful ChIP experiment is the preparation of sheared chromatin w...	Download
Deparaffinization - Procedure for FFPE nucleic acid extraction with the Bioruptor® Deparafinization of FFPE samples is typically performed using a non-polar solvent, such as xylene...	Download
DNA Shearing for Bioruptor^® Pico - Standard 100 μl Volume Standard protocols for programmable DNA size distributions, excellent reproducibility, and high d...	Download
DNA Shearing for Bioruptor® Pico - 50 μl Volume For DNA shearing in 50 μl we highly recommend to use the 0.1 ml tube holder & tube adaptor...	Download
DNA shearing for Next-Generation Sequencing with the Bioruptor® pico, 0.2 ml Bioruptor® microtubes and the corresponding holder Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, amo...	Download
DNA Shearing with Bioruptor® Pico - Small Volume (10 µl) For DNA shearing we highly recommend to use the 0.1 ml tube holder & tube adaptors (Cat. No. ...	Download
FFPE DNA extraction protocol using the Bioruptor® The number of archival formalin-fixed paraffin embedded (FFPE) samples is in the millions, provid...	Download
iST Sample Preparation with the Bioruptor® The PreOmics iST sample preparation of proteins combined with the Diagenode Bioruptor® Pico e...	Download
PCR amplicons shearing using the Bioruptor Pico With the Bioruptor® Pico and the former model Bioruptor® NGS it is possible to shear PCR ...	Download
Protein extraction from Tissues and Cultured Cells using Bioruptor® Pico Protein extraction from tissues and cultured cells is the first step for many biochemical and ana...	Download
Re-shearing of decrosslinked immunoprecipitated DNA using the Bioruptor® Pico ChIP-seq is a common tool used to study protein-DNA interactions in cells and tissues on a genome...	Download
RNA Shearing for Bioruptor® NGS and Pico The Diagenode ACT (Adaptative Cavitation Transfer technology) process is highly reproducible, how...	Download
Ultrasensitive proteomics for microdissected fresh frozen tissue samples using the Bioruptor® Pico for sample preparation Histology-defined proteomics investigations are a fundamental tool in modern molecular pathology....	Download

Applications

DNA/RNA shearing
In recent years, advances in Next-Generation Sequencing (NGS) have revolutionized genomics and biology. This growth has fueled demands on upstream techniques for optimal sample preparation and genomic library construction. One of the most critic... Read more

Chromatin shearing
The most important steps for a successful ChIP include both cell fixation and lysis, and chromatin shearing. Researchers often overlook the critical nature of both of these steps. Eliminating inconsistencies in the shearing step, Diagenode's Bio... Read more

FFPE DNA extraction
Diagenode's high yields FFPE DNA extraction using Bioruptor® is a superior method for extracting DNA for Next-Gen Sequencing. Our FFPE DNA Extraction kit contains optimized reagents that are added directly to the FFPE samples to remove paraf... Read more

Next Generation Sequencing
DNA Shearing, library preparation, and automation: your one-stop shop for NGS 1. Choose your shearing device: Shear DNA anywhere from 150 bp to 75 kb Shear down to 5 μl: 150 bp - 2 kb Perfect for NGS DNA library prep and FFPE n... Read more

ChIP-seq
Chromatin Immunoprecipitation (ChIP) coupled with high-throughput massively parallel sequencing as a detection method (ChIP-seq) has become one of the primary methods for epigenomics researchers, namely to investigate protein-DNA interaction on ... Read more

Protein extraction
Various biochemical and analytical techniques require the extraction of protein from tissues or mammalian, yeast and bacterial cells. Obtaining high quality and yields of proteins is important for further downstream protein characterization such... Read more

Methylbinding domain protein
The MBD approach is based on the very high affinity of a H6-GST-MBD fusion protein for methylated DNA. This protein consists of the methyl binding domain (MBD) of human MeCP2, as a C-terminal fusion with Glutathione-S-transferase (GST) containin... Read more

Chromatin Analysis
Chromatin immunoprecipitation (ChIP) is a method used to determine the location of genome binding sites for a specific protein of interest, giving invaluable insights into the regulation of gene expression. ChIP involved the selective enrichme... Read more

Documents

Bioruptor^® Sonicator Brochure BROCHURE Diagenode’s Bioruptor® uses state-of-the-art shearing device to disrupt, disp...	Download
Bioruptor® DNA shearing for Agilent SureSelect library preparation: a perfect combination APPLICATION NOTE The Cologne Center for Genomics (CCG), headed by Prof. Dr. Peter Nürnberg, shows that t...	Download
Which tubes for which Bioruptor^®? QUICK GUIDE Diagenode tubes were developed specifically for use with the Bioruptor®. They ensure a maximu...	Download
Bioruptor^® NGS: Unbiased DNA shearing for Next-Generation Sequencing CASE STUDY Wouter Coppieters, PhD, and his colleagues operate the genomics core facility at the GIGA center,...	Download
True MicroChIP and MicroPlex kits APPLICATION NOTE From minuscule amounts to magnificent results: reliable ChIP-seq data from 10,000 cells with the ...	Download
ChIP-seq from human tumor tissue APPLICATION NOTE Application of the Bioruptor® Pico for shearing chromatin fragments for ChIP-seq from human t...	Download
ChIP kit results with True MicroChIP kit POSTER Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the g...	Download
Bioruptor^® NGS System – Designed Exclusively for Fast & Accurate DNA Shearing POSTER The Bioruptor®NGS is the DNA shearing device of choice for sequencing applications, providing...	Download
Application of the Bioruptor® Pico for best shearing of yeast genomic DNA for NGS APPLICATION NOTE DNA shearing is important step for next-generation sequencing library preparation. Important is r...	Download
DNA shearing for Next-Generation Sequencing with the Bioruptor® pico, 0.2 ml Bioruptor® microtubes and the corresponding holder PROTOCOL Optimal data generation using NGS platforms relies on a few sample-preparation prerequisites, amo...	Download
Chromatin shearing with the Bioruptor® Pico, 0.2 ml Bioruptor® Microtubes and the corresponding holder PROTOCOL The first critical step of a successful ChIP experiment is the preparation of sheared chromatin w...	Download
Workflow for FFPE-derived DNA shearing prior to Next Generation Sequencing APPLICATION NOTE Formalin fixation and paraffin embedding (FFPE) is a standard method for long-term preservation o...	Download
Efficient and streamlined solution for high-quality NGS library preparation using the Bioruptor® Pico and JetSeqTM Flex DNA Library Preparation Kit APPLICATION NOTE Next Generation Sequencing workflows include a number of critical steps which can have a signific...	Download
Comparison of the S. cerevisae chromatin shearing with Covaris™ S2 and Bioruptor® Pico APPLICATION NOTE The chromatin shearing is very important step for all kind of ChIP analysis followed by next-gene...	Download
Ultrasensitive proteomics for microdissected fresh frozen tissue samples APPLICATION NOTE This protocol, specifically designed for ultrasensitive proteomics, enables high throughput quant...	Download
Bioruptor® Pico Sonication System Manual MANUAL The Bioruptor® Pico is the latest innovation in shearing and represents a new breakthrough as...	Download

Publications

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Corticosteroid receptors adopt distinct cyclical transcriptional signatures
Florian Le Billan, Larbi Amazit, Kevin Bleakley, Qiong-Yao Xue, Eric Pussard, Christophe Lhadj, Peter Kolkhof, Say Viengchareun, Jérôme Fagart, and Marc Lombès
Mineralocorticoid receptors (MRs) and glucocorticoid receptors (GRs) are two closely related hormone-activated transcription factors that regulate major pathophysiologic functions. High homology between these receptors accounts for the crossbinding of their corresponding ligands, MR being activated by both aldostero...

BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
Arts RJW, Moorlag SJCFM, Novakovic B, Li Y, Wang SY, Oosting M, Kumar V, Xavier RJ, Wijmenga C, Joosten LAB, Reusken CBEM, Benn CS, Aaby P, Koopmans MP, Stunnenberg HG, van Crevel R, Netea MG
The tuberculosis vaccine bacillus Calmette-Guérin (BCG) has heterologous beneficial effects against non-related infections. The basis of these effects has been poorly explored in humans. In a randomized placebo-controlled human challenge study, we found that BCG vaccination induced genome-wide epigenetic repr...

Modulation of p53 and met expression by Krüppel-like factor 8 regulates zebrafish cerebellar development.
Tsai MY, Lu YF, Liu YH, Lien HW, Huang CJ, Wu JL, Hwang SL
Krüppel-like factor 8 (Klf8) is a zinc-finger transcription factor implicated in cell proliferation, and cancer cell survival and invasion; however, little is known about its role in normal embryonic development. Here, we show that Klf8 is required for normal cerebellar development in zebrafish embryos. Morphol...