Diagenode

MicroPlex Library Preparation Kit v2 (48 indexes)

Catalog Number
Format
Price
C05010014
(C05010011)
48 rxns
$2,800.00

Specifically optimized for ChIP-seq

The MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allows the preparation of indexed libraries from just picogram inputs. In combination with the True MicroChIP kit, it allows for performing ChIP-seq on as few as 10,000 cells. Less input, fewer steps, fewer supplies, faster time to results! 

TESTIMONIAL

We used the MicroPlex version 2 kit to generate libraries using ChIP DNA for several transcription factors and compared the results to a standard library generation protocol starting from 5ng of ChIP DNA. Even when we reduced the starting amount of DNA by 10-fold, the MicroPlex Kit produced the same high yields and quality of the libraries. As expected, the number of duplicate reads increased but 15 to 20 million unique reads were sufficient to achieve excellent enrichment data. We found that no information was lost, and the MicroPlex Kit helped produce data that was consistent with the standard protocol despite the lower input. On top of this, the MicroPlex Kit was extremely user-friendly and saved us time. The MicroPlex version 2 kit will make challenging ChIP-seq experiments that rely on very limited amount of starting material much easier with robust results.

Katia Basso, PhD, Assistant Professor, Columbia University, New York
  • Characteristics
    • 1 tube, 2 hours, 3 steps protocol
    • Picogram inputs
    • Reduce potential bias - few PCR amplification cycles needed
    • High sensitivity ChIP-seq - low PCR duplication rate
    • Great multiplexing flexibility with 48 barcodes (8 nt) included
    • Automatable

    MicroPlex v1 MicroPlex v2
    Sensitivity ++ +++
    PCR cycles (50 pg starting material) 20 16
    Index sequences 6 nucleotides 8 nucleotides
    PCR reaction volume 75 µl 50 µl

    Reliable detection of enrichments in ChIP-seq

    Reliable detection of enrichments in ChIP-seq figure 1

    Figure A. ChIP has been peformed with H3K4me3 antibody, amplification of 17 pg of DNA ChIP'd from 10.000 cells and amplification of 35 pg of DNA ChIP'd from 100.000 cells (control experiment). The IP'd DNA was amplified and transformed into a sequencing-ready preparation for the Illumina plateform with the MicroPlex Library Preparation kit. The library was then analysed on an Illumina® Genome Analyzer. Cluster generation and sequencing were performed according to the manufacturer's instructions.

    Reliable detection of enrichments in ChIP-seq figure 2

    Figure B. We observed a perfect match between the top 40% of True MicroChIP peaks and the reference dataset. Based on the NIH Encode project criterion, ChIP-seq results are considered reproducible between an original and reproduced dataset if the top 40% of peaks have at least an 80% overlap ratio with the compared dataset.

  •  Testimonials

    We sheared the DNA on the Diagenode One and used the MicroPlex Library Preparation v2 Kit to create DNA libraries for whole genome sequencing of four plant species for which there is no reference genome available. Previous attempts with a commercial Tn5-transposase based method gave unsatisfactory results. However, the Diagenode MicroPlex kit was quicker, easier, and gave the expected profile of fragment sizes. In just 30 seconds of sonication, we obtained a fragment distribution centered at 270 bp. The library construction took only 2 hours with this kit. The library was sequenced in a NexSeq 550 in High-Output mode, giving 85% based with>Q30.

    PhD. Ricardo Verdugo, Assistant Professor, University of Chile

    There are so many ChIP-related products on the market, but I feel so lucky that I have been using the ones from Diagenode since I started my CHIP-seq project. I have used their iDeal CHIP-seq Kit for Transcription Factors and MicroPlex Library Prep Kit v2. Both of them are fantastic and very reproducible. With the very-well written protocols, you will just be home and dry. Particularly, I want to thank the technical support, who is very patient, knowledgeable and extremely helpful. I would definitely recommend my colleagues to use the CHIP products from Diagenode.

    Dr Kaiyu Lei, Faculty of Medicine, Department of Surgery & Cancer, Imperial College London

    I am working with the True MicroChIP & Microplex Library Preparation Kits and several histone modification antibodies like H3K27ac, H3K4me3, H3K36me3, and H3K27me3. I got always very good and reproducible results for my ChIP-seq experiments.

    Andrea Thiesen, ZMB, Developmental Biology, Prof. Dr. Andrea Vortkamp´s lab, University Duisburg-Essen, Germany

    The Diagenode MicroPlex kit is an efficient way to make sequencing libraries, especially from samples with very low inputs. We used it for successfully processing ChIP material of transcription factors and histone modifications.

    Dr. Filippo Cernilogar (Ludwig-Maximilian-Universität München, Germany)

    The Diagenode MicroPlex kit is the quickest and most efficient way to make sequencing libraries, especially from samples with very low inputs. We regularly start with picogram amounts of ChIP material and produce excellent quality libraries that would be impossible to make using normal methods. Sequencing libraries made from the MicroPlex kit give us excellent results even in large genomes. The kit performs very well, and we will use the kit in the future for studies with low cell numbers or starting material.

    Dr. Morgan Sammons, Lab of Dr. Shelley Berger, University of Pennsylvania
  •  Applications
    DNA/RNA library preparation
    Most of the major next-generation sequencing platforms require ligation of specific adaptor oligos to fragmented DNA or RNA prior to sequencing After input DNA has been fragmented, it is end-repaired and blunt-ended. The next step is a A-tail... 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 libr... Read more
  •  Documents
    MicroPlex Library Preparation kit v2 MANUAL
    MicroPlex v2 builds on the innovative MicroPlex chemistry to generate DNA libraries with ex...
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    True MicroChIP and MicroPlex kits APPLICATION NOTE
    From minuscule amounts to magnificent results: reliable ChIP-seq data from 10,000 cells with the ...
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    ChIP kit results with True MicroChIP kit POSTER
    Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the g...
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  •  Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: MicroPlex Library Preparation Kit v2 (48 indexes) (Diagenode Cat# C05010014). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    The epigenetic basis for the impaired ability of adult murine retinal pigment epithelium cells to regenerate retinal tissue.
    Dvoriantchikova G, Seemungal RJ, Ivanov D
    The epigenetic plasticity of amphibian retinal pigment epithelium (RPE) allows them to regenerate the entire retina, a trait known to be absent in mammals. In this study, we investigated the epigenetic plasticity of adult murine RPE to identify possible mechanisms that prevent mammalian RPE from regenerating retinal...

    PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex.
    Link S, Spitzer RMM, Sana M, Torrado M, Völker-Albert MC, Keilhauer EC, Burgold T, Pünzeler S, Low JKK, Lindström I, Nist A, Regnard C, Stiewe T, Hendrich B, Imhof A, Mann M, Mackay JP, Bartkuhn M, Hake SB
    Chromatin structure and function is regulated by reader proteins recognizing histone modifications and/or histone variants. We recently identified that PWWP2A tightly binds to H2A.Z-containing nucleosomes and is involved in mitotic progression and cranial-facial development. Here, using in vitro assays, we show that...

    Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements.
    Svedberg J, Hosseini S, Chen J, Vogan AA, Mozgova I, Hennig L, Manitchotpisit P, Abusharekh A, Hammond TM, Lascoux M, Johannesson H
    Meiotic drive is widespread in nature. The conflict it generates is expected to be an important motor for evolutionary change and innovation. In this study, we investigated the genomic consequences of two large multi-gene meiotic drive elements, Sk-2 and Sk-3, found in the filamentous ascomycete Neurospora intermedi...

    Prospective Isolation and Characterization of Genetically and Functionally Distinct AML Subclones.
    de Boer B, Prick J, Pruis MG, Keane P, Imperato MR, Jaques J, Brouwers-Vos AZ, Hogeling SM, Woolthuis CM, Nijk MT, Diepstra A, Wandinger S, Versele M, Attar RM, Cockerill PN, Huls G, Vellenga E, Mulder AB, Bonifer C, Schuringa JJ
    Intra-tumor heterogeneity caused by clonal evolution is a major problem in cancer treatment. To address this problem, we performed label-free quantitative proteomics on primary acute myeloid leukemia (AML) samples. We identified 50 leukemia-enriched plasma membrane proteins enabling the prospective isolation of gene...

    Genomic Location of PRMT6-Dependent H3R2 Methylation Is Linked to the Transcriptional Outcome of Associated Genes.
    Bouchard C, Sahu P, Meixner M, Nötzold RR, Rust MB, Kremmer E, Feederle R, Hart-Smith G, Finkernagel F, Bartkuhn M, Savai Pullamsetti S, Nist A, Stiewe T, Philipsen S, Bauer UM
    Protein arginine methyltransferase 6 (PRMT6) catalyzes asymmetric dimethylation of histone H3 at arginine 2 (H3R2me2a). This mark has been reported to associate with silent genes. Here, we use a cell model of neural differentiation, which upon PRMT6 knockout exhibits proliferation and differentiation defects. S...

    Genome-wide rules of nucleosome phasing
    Sandro Baldi, Dhawal S. Jain1, Lisa Harpprecht1, Angelika Zabel1, Marion Scheibe, Falk Butter, Tobias Straub and Peter B. Becker
    Regular successions of positioned nucleosomes – phased nucleosome arrays (PNAs) – are predominantly known from transcriptional start sites (TSS). It is unclear whether PNAs occur elsewhere in the genome. To generate a comprehensive inventory of PNAs for Drosophila, we applied spectral analysis to nucleos...

    Combined cistrome and transcriptome analysis of SKI in AML cells identifies SKI as a co-repressor for RUNX1.
    Feld C, Sahu P, Frech M, Finkernagel F, Nist A, Stiewe T, Bauer UM, Neubauer A
    SKI is a transcriptional co-regulator and overexpressed in various human tumors, for example in acute myeloid leukemia (AML). SKI contributes to the origin and maintenance of the leukemic phenotype. Here, we use ChIP-seq and RNA-seq analysis to identify the epigenetic alterations induced by SKI overexpression in AML...

    A long range distal enhancer controls temporal fine-tuning of PAX6 expression in neuronal precursors.
    Lacomme M, Medevielle F, Bourbon HM, Thierion E, Kleinjan DJ, Roussat M, Pituello F, Bel-Vialar S
    Proper embryonic development relies on a tight control of spatial and temporal gene expression profiles in a highly regulated manner. One good example is the ON/OFF switching of the transcription factor PAX6 that governs important steps of neurogenesis. In the neural tube PAX6 expression is initiated in neural proge...

    EWS-FLI1 increases transcription to cause R-loops and block BRCA1 repair in Ewing sarcoma.
    Gorthi A, Romero JC, Loranc E, Cao L, Lawrence LA, Goodale E, Iniguez AB, Bernard X, Masamsetti VP, Roston S, Lawlor ER, Toretsky JA, Stegmaier K, Lessnick SL, Chen Y, Bishop AJR
    Ewing sarcoma is an aggressive paediatric cancer of the bone and soft tissue. It results from a chromosomal translocation, predominantly t(11;22)(q24:q12), that fuses the N-terminal transactivation domain of the constitutively expressed EWSR1 protein with the C-terminal DNA binding domain of the rarely expressed FLI...

    A Specific PfEMP1 Is Expressed in P. falciparum Sporozoites and Plays a Role in Hepatocyte Infection.
    Zanghì G, Vembar SS, Baumgarten S, Ding S, Guizetti J, Bryant JM, Mattei D, Jensen ATR, Rénia L, Goh YS, Sauerwein R, Hermsen CC, Franetich JF, Bordessoulles M, Silvie O, Soulard V, Scatton O, Chen P, Mecheri S, Mazier D, Scherf A
    Heterochromatin plays a central role in the process of immune evasion, pathogenesis, and transmission of the malaria parasite Plasmodium falciparum during blood stage infection. Here, we use ChIP sequencing to demonstrate that sporozoites from mosquito salivary glands expand heterochromatin at subtelomeric regions t...

    A multi-omics study of the grapevine-downy mildew (Plasmopara viticola) pathosystem unveils a complex protein coding- and noncoding-based arms race during infection.
    Brilli M, Asquini E, Moser M, Bianchedi PL, Perazzolli M, Si-Ammour A
    Fungicides are applied intensively to prevent downy mildew infections of grapevines (Vitis vinifera) with high impact on the environment. In order to develop alternative strategies we sequenced the genome of the oomycete pathogen Plasmopara viticola causing this disease. We show that it derives from a Phytophthora-l...

    MLL2 conveys transcription-independent H3K4 trimethylation in oocytes
    Hanna C.W. et al.
    Histone 3 K4 trimethylation (depositing H3K4me3 marks) is typically associated with active promoters yet paradoxically occurs at untranscribed domains. Research to delineate the mechanisms of targeting H3K4 methyltransferases is ongoing. The oocyte provides an attractive system to investigate these mechanisms, becau...

    An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells
    Berrens R.V. et al.
    Erasure of DNA methylation and repressive chromatin marks in the mammalian germline leads to risk of transcriptional activation of transposable elements (TEs). Here, we used mouse embryonic stem cells (ESCs) to identify an endosiRNA-based mechanism involved in suppression of TE transcription. In ESCs with DNA demeth...

    Epigenome profiling and editing of neocortical progenitor cells during development
    Albert M. et al.
    The generation of neocortical neurons from neural progenitor cells (NPCs) is primarily controlled by transcription factors binding to DNA in the context of chromatin. To understand the complex layer of regulation that orchestrates different NPC types from the same DNA sequence, epigenome maps with cell type resoluti...

    Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles
    Marincevic-Zuniga Y. et al.
    BACKGROUND: Structural chromosomal rearrangements that lead to expressed fusion genes are a hallmark of acute lymphoblastic leukemia (ALL). In this study, we performed transcriptome sequencing of 134 primary ALL patient samples to comprehensively detect fusion transcripts. METHODS: We combined fusion gene detec...

    Dynamics of RNA Polymerase II Pausing and Bivalent Histone H3 Methylation during Neuronal Differentiation in Brain Development
    Liu J. et al.
    During cellular differentiation, genes important for differentiation are expected to be silent in stem/progenitor cells yet can be readily activated. RNA polymerase II (Pol II) pausing and bivalent chromatin marks are two paradigms suited for establishing such a poised state of gene expression; however, their specif...

    Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation
    Pünzeler S. et al.
    Replacement of canonical histones with specialized histone variants promotes altering of chromatin structure and function. The essential histone variant H2A.Z affects various DNA-based processes via poorly understood mechanisms. Here, we determine the comprehensive interactome of H2A.Z and identify PWWP2A as a novel...

    Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
    Thierion E. et al.
    Developmental genes can harbour multiple transcriptional enhancers that act simultaneously or in succession to achieve robust and precise spatiotemporal expression. However, the mechanisms underlying cooperation between cis-acting elements are poorly documented, notably in vertebrates. The mouse gene Krox20 encodes ...

    Ectopic application of the repressive histone modification H3K9me2 establishes post-zygotic reproductive isolation in Arabidopsis thaliana
    Jiang H. et al.
    Hybrid seed lethality as a consequence of interspecies or interploidy hybridizations is a major mechanism of reproductive isolation in plants. This mechanism is manifested in the endosperm, a dosage-sensitive tissue supporting embryo growth. Deregulated expression of imprinted genes such as ADMETOS (ADM) underpin th...

    2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD)-elicited effects on bile acid homeostasis: Alterations in biosynthesis, enterohepatic circulation, and microbial metabolism.
    Fader K. et al.
    2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental contaminant which elicits hepatotoxicity through activation of the aryl hydrocarbon receptor (AhR). Male C57BL/6 mice orally gavaged with TCDD (0.01-30 µg/kg) every 4 days for 28 days exhibited bile duct proliferation and perichola...

    CRISPR/Cas9 Genome Editing Reveals That the Intron Is Not Essential for var2csa Gene Activation or Silencing in Plasmodium falciparum
    Bryant J.M. et al.
    Plasmodium falciparum relies on monoallelic expression of 1 of 60 var virulence genes for antigenic variation and host immune evasion. Each var gene contains a conserved intron which has been implicated in previous studies in both activation and repression of transcription via several epigenetic mechanisms, includin...

    TIAM1 Antagonizes TAZ/YAP Both in the Destruction Complex in the Cytoplasm and in the Nucleus to Inhibit Invasion of Intestinal Epithelial Cells
    Diamantopoulou Z. et al.
    Aberrant WNT signaling drives colorectal cancer (CRC). Here, we identify TIAM1 as a critical antagonist of CRC progression through inhibiting TAZ and YAP, effectors of WNT signaling. We demonstrate that TIAM1 shuttles between the cytoplasm and nucleus antagonizing TAZ/YAP by distinct mechanisms in the two compartmen...

    The Drosophila speciation factor HMR localizes to genomic insulator sites
    Gerland T.A. et al.
    Hybrid incompatibility between Drosophila melanogaster and D. simulans is caused by a lethal interaction of the proteins encoded by the Hmr and Lhr genes. In D. melanogaster the loss of HMR results in mitotic defects, an increase in transcription of transposable elements and a deregulation of heterochromatic genes. ...

    Nitric oxide modulates histone acetylation at stress genes by inhibition of histone deacetylases
    Mengel A. et al.
    Histone acetylation, which is an important mechanism to regulate gene expression, is controlled by the opposing action of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In animals, several HDACs are subjected to regulation by nitric oxide (NO), in plants however, it is unknown whether NO affects...

    Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells
    Koppens MA et al.
    BACKGROUND & AIMS: The polycomb repressive complex 2 (PRC2) regulates differentiation by contributing to repression of gene expression and thereby stabilizing the fate of stem cells and their progeny. PRC2 helps to maintain adult stem cell populations, but little is known about its functions in intestinal stem ...

    Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells
    von Meyenn F et al.
    Global demethylation is part of a conserved program of epigenetic reprogramming to naive pluripotency. The transition from primed hypermethylated embryonic stem cells (ESCs) to naive hypomethylated ones (serum-to-2i) is a valuable model system for epigenetic reprogramming. We present a mathematical model, which accu...

    Pyruvate kinase isoform switching and hepatic metabolic reprogramming by the environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)
    Rance Nault, Kelly A. Fader, Mathew P. Kirby, Shaimaa Ahmed, Jason Matthews, Daniel Jones, Sophia Y. Lunt
    The environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) elicits dose-dependent hepatotoxicity that includes fat accumulation, inflammation, and fibrosis that may progress to hepatocellular carcinoma. To further investigate these effects, RNA-Seq data was integrated with computationally identified pu...

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