MicroPlex Library Preparation Kit v2 (12 indices)

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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! 


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

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
  • 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 12 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

    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

    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

    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 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
  • Protocols
    MicroPlex Library Preparation kit™ v2 - IP-Star Compact
    The “MicroPlex Library Preparation” protocol on the IP-Star® is using the standar...
  • 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 QUICK GUIDE
    MicroPlex Library Preparation v2 builds on the innovative MicroPlex chemistry to generate...
    MicroPlex Library Preparation kit v2 MANUAL
    MicroPlex v2 builds on the innovative MicroPlex chemistry to generate DNA libraries with ex...
    True MicroChIP and MicroPlex kits APPLICATION NOTE
    From minuscule amounts to magnificent results: reliable ChIP-seq data from 10,000 cells with the ...
    ChIP kit results with True MicroChIP kit POSTER
    Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) has become the g...
    MicroPlex v2 - 12 indices PDF
    MicroPlex v2 - 12 indices
  • Publications

    How to properly cite this product in your work

    Diagenode strongly recommends using this: MicroPlex Library Preparation Kit v2 (12 indices) (Diagenode Cat# C05010012). Click here to copy to clipboard.

    Using our products in your publication? Let us know!

    Genome-wide mapping and analysis of aryl hydrocarbon receptor (AHR)- and aryl hydrocarbon receptor repressor (AHRR)-binding sites in human breast cancer cells
    Sunny Y. Yang, Shaimaa Ahmed, Somisetty V. Satheesh, Jason Matthews
    The aryl hydrocarbon receptor (AHR) mediates the toxic actions of environmental contaminants, such as 2,3,7,8-tetrachlorodibenzo-ρ-dioxin (TCDD), and also plays roles in vascular development, the immune response, and cell cycle regulation. The AHR repressor (AHRR) is an AHR-regulated gene and a negative regulato...

    RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA(+) and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells.
    Lund R.J. et al.
    POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maintenance of stem cell state through mechanisms not known in detail. To explore how POLR3G regulates stem cell state, we carried out deep-sequencing analysis of polyA+ and smallRNA transcriptomes present in hPSCs an...

    Epigenetically-driven anatomical diversity of synovial fibroblasts guides joint-specific fibroblast functions
    Frank-Bertoncelj M, Trenkmann M, Klein K, Karouzakis E, Rehrauer H, Bratus A, Kolling C, Armaka M, Filer A, Michel BA, Gay RE, Buckley CD, Kollias G, Gay S, Ospelt C
    A number of human diseases, such as arthritis and atherosclerosis, include characteristic pathology in specific anatomical locations. Here we show transcriptomic differences in synovial fibroblasts from different joint locations and that HOX gene signatures reflect the joint-specific origins of mouse and human synov...

    First landscape of binding to chromosomes for a domesticated mariner transposase in the human genome: diversity of genomic targets of SETMAR isoforms in two colorectal cell lines
    Antoine-Lorquin A. et al.
    Setmar is a 3-exons gene coding a SET domain fused to a Hsmar1 transposase. Its different transcripts theoretically encode 8 isoforms with SET moieties differently spliced. In vitro, the largest isoform binds specifically to Hsmar1 DNA ends and with no specificity to DNA when it is associated with hPso4. In colon ce...

    Crebbp loss cooperates with Bcl2 over-expression to promote lymphoma in mice
    Idoia García-Ramírez, Saber Tadros, Inés González-Herrero, Alberto Martín-Lorenzo, Guillermo Rodríguez-Hernández, Dalia Moore, Lucía Ruiz-Roca, Oscar Blanco, Diego Alonso-López, Javier De Las Rivas, Keenan Hartert, Romain Duval, David Klinkebiel, Martin B
    CREBBP is targeted by inactivating mutations in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). Here, we provide evidence from transgenic mouse models that Crebbp deletion results in deficits in B-cell development and can cooperate with Bcl2 over-expression to promote B-cell lymphoma. Through tra...

    Aorta macrophage inflammatory and epigenetic changes in a murine model of obstructive sleep apnea: Potential role of CD36.
    Cortese R. et al.
    Obstructive sleep apnea (OSA) affects 8-10% of the population, is characterized by chronic intermittent hypoxia (CIH), and causally associates with cardiovascular morbidities. In CIH-exposed mice, closely mimicking the chronicity of human OSA, increased accumulation and proliferation of pro-inflammatory metabolic M1...

    Intestinal NCoR1, a regulator of epithelial cell maturation, controls neonatal hyperbilirubinemia
    Chen S. et al.
    Severe neonatal hyperbilirubinemia (SNH) and the onset of bilirubin encephalopathy and kernicterus result in part from delayed expression of UDP-glucuronosyltransferase 1A1 (UGT1A1) and the inability to metabolize bilirubin. Although there is a good understanding of the early events after birth that lead to the rapi...

    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. ...

    BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire
    Najafova Z. et al.
    Proper temporal epigenetic regulation of gene expression is essential for cell fate determination and tissue development. The Bromodomain-containing Protein-4 (BRD4) was previously shown to control the transcription of defined subsets of genes in various cell systems. In this study we examined the role of BRD4 in pr...

    CTCF modulates Estrogen Receptor function through specific chromatin and nuclear matrix interactions
    Fiorito E. et al.
    Enhancer regions and transcription start sites of estrogen-target regulated genes are connected by means of Estrogen Receptor long-range chromatin interactions. Yet, the complete molecular mechanisms controlling the transcriptional output of engaged enhancers and subsequent activation of coding genes remain elusive....

    PionX sites mark the X chromosome for dosage compensation
    Villa R et al.
    The rules defining which small fraction of related DNA sequences can be selectively bound by a transcription factor are poorly understood. One of the most challenging tasks in DNA recognition is posed by dosage compensation systems that require the distinction between sex chromosomes and autosomes. In Drosophila mel...

    reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells
    Kinkley S et al.
    The combinatorial action of co-localizing chromatin modifications and regulators determines chromatin structure and function. However, identifying co-localizing chromatin features in a high-throughput manner remains a technical challenge. Here we describe a novel reChIP-seq approach and tailored bioinformatic analys...

    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...

    Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm
    Moreno-Romero J et al.
    Parental genomes in the endosperm are marked by differential DNA methylation and are therefore epigenetically distinct. This epigenetic asymmetry is established in the gametes and maintained after fertilization by unknown mechanisms. In this manuscript, we have addressed the key question whether parentally inherited...

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