Diagenode

NGS Library preparation

Library preparation for ChIP-seq

Library preparation following ChIP can be challenging due to the limited amount of DNA recovered after ChIP. In order to provide the optimal solution for ChIP-seq, Diagenode has developed the MicroPlex Library Preparation Kit, specifically designed for reliable library preparation from limited DNA inputs. The iDeal Library Preparation Kit is also available for use with standard inputs. Combine our library preparation kits with the iDeal ChIP-seq and the True MicroChIP kits for best ChIP-seq results.

Diagenode’s MicroPlex Library Preparation kits have been extensively validated for ChIP-seq samples. Generated libraries are compatible with single-end or paired-end sequencing. MicroPlex chemistry (using stem-loop adapters ) is specifically developed and optimized to generate DNA libraries with high molecular complexity from the lowest input amounts. Only 50 pg to 50 ng of fragmented double-stranded DNA is required for library preparation. The entire three-step workflow takes place in a single tube or well in about 2 hours. No intermediate purification steps and no sample transfers are necessary to prevent handling errors and loss of valuable samples.

Features

  • Sample: Fragmented dsDNA
  • Low input: 50 pg – 50 ng
  • Fast protocol: 2 hours
  • Easy processing: 3 steps in 1 tube
  • No intermediate purification
  • Sequencing technology: Illumina
  • Manual and automated protocols available

Applications

  • ChIP-seq library prep from ChIP-derived DNA
  • Low input DNA sequencing

Two versions are available:

The iDeal Library Preparation Kit reliably converts DNA into indexed libraries for next-generation sequencing, with input amounts down to 5 ng. Our kit offers a simple and fast workflow, high yields, and ready-to-sequence DNA on the Illumina platform.

Features

  • Sample: Fragmented dsDNA
  • Input: 5 ng – 1 µg
  • Fast protocol: 3 hours
  • Easy processing: 3 steps
  • Indexing: single indexes for multiplexing up to 24 samples
  • Manual and automated protocols available
  • Sequencing technology: Illumina

Applications

  • MeDIP-seq library prep
  • Genomic DNA sequencing
  • High input ChIP-seq
Cat. No. Product Format
C05010020 iDeal Library Preparation Kit x24 (incl. Index Primer Set 1) 24 rxns
C05010021 Index Primer Set 2 (iDeal Lib. Prep Kit x24) 24 rxns

How to choose your library preparation kit?

Application

ChIP-seq library prep
Low input DNA sequencing

MeDIP-seq library prep
Genomic DNA sequencing
High input ChIP-seq

DNA input

Low
(50 pg – 50 ng)

Standard
(5 ng – 1 µg)

Multiplexing

Up to 384 samples

Up to 48 samples

Up to 24 samples

Indexes

Dual indexes (DI)

Single indexes (SI)

Single indexes (SI)

Kit

MicroPlex Library Preparation Kit v3
(dual indexes not included in the kit)

Kit
C05010001 - 48 rxns
C05010002 - 96 rxns

Dual indexes
C05010003 - 24 DI/ 48 rxns
C05010004 - Set I 96 DI/ 96 rxns
C05010005 - Set II 96 DI/ 96 rxns
C05010006 - Set III 96 DI/ 96 rxns
C05010007 - Set IV 96 DI/ 96 rxns

MicroPlex Library Preparation Kit v2
(single indexes included in the kit)

C05010012 - 12 SI/ 12 rxns
C05010013 - 12 SI/ 48 rxns
C05010014 - 48 SI/ 48 rxns

iDeal Library Preparation Kit
(Set 1 of indexes included in the kit)

C05010020 - 12 SI/ 24 rxns

Index Primer Set 2

C05010021 - 12 SI/ 24 rxns

Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has become the gold standard to investigate genome-wide epigenetic profiles. However, ChIP from a limited amount of cells has been a challenge. Here we provide a complete and robust workflow solution for successful ChIP-seq from small numbers of cells using the True MicroChIP kit and MicroPlex Library Preparation kit.

APPLICATION NOTE

ChIP efficiency on 10,000 cells

From minuscule amounts to magnificent results:
reliable ChIP-seq data from 10,000 cells with the True MicroChIP™ and the MicroPlex Library Preparation™ kits.

DOWNLOAD
APPLICATION NOTE

Quality control check of a ChIP-seq library on the Fragment Analyzer. High Efficiency ChIP performed on 10,000 cells

Best Workflow Practices for ChIP-seq Analysis with Small Samples

DOWNLOAD

MicroPlex Library Preparation Kit

  1. Can I use the available Illumina primers and validate them with the MicroPlex Kit v2?
    Although the final flanking sequences of MicroPlex are the same as those used by Illumina, the PCR primers are not identical and part of them is supplied with the buffer. For this reason Illumina primers will not work as substitute.

  2. The BioAnalyzer profile of purified library shows the presence of low molecular weight peaks (primers/adaptors) in the samples. Should I re- purify the samples or they can be used directly to the sequencing? If the second purification is recommended, which ratio sample/AMPure beads should I use?
    You can do a second round of purification using 1:1 ratio of AMPure beads to sample and this should get rid of the majority of the dimers.

  3. I am going to use the MicroPlex Library Preparation Kit v2 on ChIP samples . Our thermocycler has ramp rate 1.5°/s max while the protocol recommends using a ramp rate 3 to 5°/s. How would this affect the library prep?
    We have not used a thermocycler with a ramp rate of 1.5 °C, which seems faster than most of thermocyclers. Too fast of a ramp rate may affect the primer annealing and ligation steps.

  4. What is the function of the replication stop site in the adapter loops?
    The replication stop site in the adaptor loops function to stop the polymerase from continuing to copy the rest of the stem loop.

  5. I want to do ChIP-seq. Which ChIP-seq kit can I use for sample preparation prior to Microplex Library Preparation Kit v2?
    In our portfolio there are several ChIP-seq kits compatible with Microplex Library Preparation Kit v2. Depending on your sample type and target studied you can use the following kits: iDeal ChIP-seq Kit for Transcription Factors (Cat. No. C01010055), iDeal ChIP-seq Kit for Histones (Cat. No. C01010051), True MicroChIP kit (Cat. No. C01010130), Universal Plant ChIP-seq Kit (Cat. No. C01010152). All these kits exist in manual and automated versions.

  6. Is Microplex Library Preparation Kit v2 compatible with exome enrichment methods?
    Microplex Library Preparation Kit v2 is compatible with major exome and target enrichment products, including Agilent SureSelect®, Roche NimbleGen® SeqCap® EZ and custom panels.

  7. What is the nick that is mentioned in the kit method overview?
    The nick is simply a gap between a stem adaptor and 3’ DNA end, as shown on the schema in the kit method overview.

  8. Are the indexes of the MicroPlex library preparation kit v2 located at i5 or i7?
    The libraries generated with the MicroPlex kit v2 contain indices located at i7.

  9. Is there a need to use custom index read primers for the sequencing to read the 8nt iPCRtags?
    There is no need for using custom Sequencing primer to sequence MicroPlex libraires. MicroPlex libraries can be sequenced using standard Illumina Sequencing kits and protocols.

  10. What is the advantage of using stem-loop adapter in the MicroPlex kit?
    There are several advantages of using stem-loop adaptors. First of all, stem-loop adaptors prevent from self-ligation thus increases the ligation efficiency between the adapter and DNA fragment. Moreover, the background is reduced using ds adaptors with no single-stranded tails. Finally, adaptor-adaptor ligation is reduced using blocked 5’ ends.

IDeal Library Preparation Kit

  1. Are the index from the iDeal library Prep kit compatible with the MicroPlex library prep kit?
    No, it is important to use only the indexes provided in the MicroPlex kit to ensure proper library preparation with this kit

Products

Cat. No.ProductFormatPrice
C05010003 24 Dual indexes for MicroPlex Kit v3 /48 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq library prep from ChIP-derived DNA. The kit MicroPlex v3...
48 rxns $380.00
C05010004 96 Dual indexes for MicroPlex Kit v3 – Set I /96 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq library prep from ChIP-derived DNA. The kit MicroPlex v3...
96 rxns $1,155.00
C05010005 96 Dual indexes for MicroPlex Kit v3 – Set II /96 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq library prep from ChIP-derived DNA. The kit MicroPlex v3...
96 rxns $1,155.00
C05010006 96 Dual indexes for MicroPlex Kit v3 – Set III /96 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq library prep from ChIP-derived DNA. The kit MicroPlex v3...
96 rxns $1,155.00
C05010007 96 Dual indexes for MicroPlex Kit v3 – Set IV /96 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq library prep from ChIP-derived DNA. The kit MicroPlex v3...
96 rxns $1,155.00
C05010001 MicroPlex Library Preparation Kit v3 /48 rxns
Diagenode’s MicroPlex Library Preparation Kits v3 have been extensively validated for ChIP-seq samples and are optimized to generate DNA libraries with...
48 rxns $1,400.00
C05010020 iDeal Library Preparation Kit x24 (incl. Index Primer Set 1)
The iDeal Library Preparation Kit reliably converts DNA into indexed libraries for next-generation sequencing, with input amounts down to 5 ng. Our kit offer...
24 rxns $925.00
C05010021 Index Primer Set 2 (iDeal Library Preparation Kit x24)
The Index Primer Set 2 (iDeal Library Preparation Kit x24) contains an additional set of 12  indexes to be used in combination with the iDeal Library Pr...
24 rxns $200.00
C05010012 MicroPlex Library Preparation Kit v2 (12 indexes)
Specifically optimized for ChIP-seqThe MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allow...
12 rxns $800.00
C05010014 MicroPlex Library Preparation Kit v2 (48 indexes)
Specifically optimized for ChIP-seqThe MicroPlex Library Preparation™ kit is the only kit on the market which is validated for ChIP-seq and which allow...
48 rxns $2,800.00

Events

  • A Century of Genetics
    Edinburgh
    Nov 13-Nov 15, 2019
  • EMEA User Group Meeting - PacBio
    Barceló Hotel, Milan, Italy
    Nov 14-Nov 15, 2019
 See all events

       Site map   |   Contact us   |   Conditions of sales   |   Conditions of purchase   |   Privacy policy   |   Diagenode Diagnostics