CHROMATIN
I. Chromatin immunoprecipitation• ChIP & ChIP-seq• Chromatin shearing• DNA purification• Library preparation
II. Tagmentation-based technologies• ATAC-seq• ChIPmentation• CUT&Tag
III. Validated antibodies

TOGETHER,WE BRING EPIGENETICS
WORKFLOWS TO NEW FRONTIERSPAGE 3

Diagenode helps you master
Chromatin Analysis

Chromosome

Chromatin structure plays a key role in regulating gene expression
by making DNA accessible to transcriptional machinery andtranscription factors. The packaging of DNA into nucleosomes forms
a closed structure that is not highly accessible to transcriptional
elements whereas the open nucleosome structure allows DNA tobe accessible.
Diagenode offers a number of solutions to help you analyze
chromatin and the role of transcriptional machinery including ChIP
kits, library preparation kits, ChIPmentation kits, CUT&Tag kit andpA-Tn5, antibodies and ATAC-seq kits.

H3K9me3
H3K27me3
H4K20me3
HETEROCHROMATIN"Silent"

Histone tailHistone post-translational modification
Transcription Factor

TF

TF
TF

Nucleosome

EUCHROMATIN"Active"
H3K4me3
H3K36me3
H4K79me3
Histone acetylations

www.diagenode.com |PAGE 4

I. Chromatin immunoprecipitation
Chromatin immunoprecipitation (ChIP) determines the location of DNA binding sites on the genome for a protein of interest, giving insights
into gene expression regulation. ChIP involves the selective enrichment of a chromatin fraction containing a specific antigen. Antibodies thatrecognize a protein or protein modification are used to determine the relative abundance of that antigen at a specific locus or loci.
With an exclusive focus on epigenetics, Diagenode provides the highest quality epigenetics products on the market. Our complete suite of
ChIP and ChIP-seq solutions includes extensively validated ChIP and ChIP-seq grade antibodies, chromatin shearing devices (Bioruptor®),kits for chromatin shearing, specialized kits for ChIP and ChIP-seq as well as for library preparation.

Step 1

Step 2

Step 3

Step 4

Step 5

Step 6

Cross link to fix
proteins to DNA

Shear chromatin

Immunoprecipitate with antibody
and magnetic beads

Reverse crosslinks
and purify

Analyze by qPCR

Prepare the libraries
for NGSNGS

All-in-one ChIP-seq:µChIPmentation for Histones (C01011011)
ChIPmentation for Histones (C01011009)
MicroPlex Library Prep. kit

True MicroChIP-seq kit (C01010132)
iDeal ChIP-seq for Histones (C01010051)
iDeal ChIP-seq for Transcription Factors (C01010055)
Universal Plant ChIP-seq kit (C01010152)

qPCR

Available
separately

Complete solutions

Workflow

Optimal solutions for your end-to-end ChIP

TAG kit for ChIPmentation
Primer indexes for
multiplexing

iDeal ChIP-qPCR (C01010180)
iDeal ChIP-FFPE (C01010190)
ChIP Cross-link Gold
(C01019027)

Equipment
Services

Innovating Epigenetics Solutions

Chromatin EasyShear Kit• High SDS (C01020012)• Low SDS (C01020013)• Ultra Low SDS (C01020010)• Plant version (C01020014)

ChIP & ChIP-seq grade Antibodies
Positive ChIP controls: H3K4me3
and CTCF antibody
Negative ChIP controls: Rabbit andMouse IgG
Magnetic beads
Magnetic rack (0,2 ml)

N/A

IPure kit v2 (C03010014)
MicroChIP DiaPure
columns (C03040001)

Bioruptor Pico
Chromatin Profiling Services

Primer pairs

MicroPlex Library Prep. kit
TAG kit for ChIPmentation
Primer indexes for
multiplexing

PAGE 5I.I Chromatin preparation

9 Obtain perfect fragment size forhigh quality ChIP Magnetic beads formore reproducible results

A successful chromatin preparation relies on the optimization of cross-linking, cell lysis
and sonication. Our Chromatin EasyShear Kits together with the Bioruptor ultrasonicator
combine efficient cell lysis and chromatin shearing leading to consistent results.

9 Keep the epitopes accessible to theantibody
9 Get consistent results from different
samples and runs

Each Chromatin EasyShear Kit provides optimized reagents and a thoroughly validated
protocol according to your specific experimental needs. SDS concentration is adapted toeach workflow taking into account target-specific requirements.

9 Benefit from the optimal kit for yourspecific experimental needs

FEATURES

KITS
Chromatin EasyShear Kit
Ultra Low SDS

Chromatin EasyShear Kit
Low SDS

Chromatin EasyShear Kit
for Plant

Chromatin EasyShear Kit
High SDS

Cat. No.

C01020010

C01020013

C01020014

C01020012

Sample type

Cells, tissue

Cells, tissuePlant tissue

Cells

TargetHistones

TF

Histones

Histones

Amount of starting material

Standard

Standard

Low and standard

Low

Nuclei isolation

Yes

Yes

Yes

No

SDS concentration‹ 0.1%

0.2%

0.5%

1%

Corresponding to shearing buffers from • iDeal ChIP-seq Kit for
Histones• ChIPmentation Kit for
Histones• iDeal ChIP-seq Kit forTranscription Factors• iDeal ChIP-qPCR Kit• iDeal ChIP-FFPE Kit• Universal Plant ChIP-seq
Kit• True MicroChIP-seq Kit• µChIPmentation for
Histones

The shearing device of choice for chromatin preparation for ChIP
The Bioruptor is the latest innovation in shearing and represents a new breakthrough as all-in-one shearing
system that delivers optimal and reproducible chromatin shearing while preserving high protein integrity.
Visit our website to learn more about our different models of Bioruptor and their features.

www.diagenode.com |PAGE 6

9 Optimized robust protocols

I.II Chromatin immunoprecipitation kits

9 Magnetic beads for more
reproducible results

Diagenode's optimized, high performance ChIP kits are the result of over 15 years of researchand development. We provide a flexible platform that addresses specific research needs witha vast array of optimized ChIP kits. In addition, we provide the industry's most validated ChIP
and ChIP-seq antibodies using a large variety of validation methods.

9 Perfect match of sequencing resultswith reference dataset
9 Many species tested (human, mouse,rat, horse, chicken, cow, pig, plants
and more)

Which ChIP kit is right?
Sample type

Application
qPCR

Sample type, target, #cell/IP
Cell/Tissue

H, TF

H <100K

Cell/ Tissue
Cell

H >100K

Kit

iDeal ChIP-qPCR Kit

Compatible library prep. kit

NAµChIPmentation Kit for Histones

Tagmentation module
included in the kit

True MicroChIP-seq Kit

Available separately

ChIPmentation Kit for Histones

Tagmentation module
included in the kit

iDeal ChIP-seq Kit for Histones
TF

NGS

H

iDeal ChIP-seq Kit
for Transcription Factors
iDeal ChIP-seq Kit for Histones

Tissue
TF

FFPE
Plant
Yeast
Innovating Epigenetics Solutions

qPCR/NGS*

H, TF

qPCR/NGSH

qPCR/NGS

H, TF*The quality of sequencing data depends on the quality of the FFPE sample

iDeal ChIP-seq Kit
for Transcription Factors
iDeal ChIP-FFPE Kit
Universal Plant ChIP-seq Kit
iDeal ChIP-seq Kit
for Transcription Factors
H: Histones

TF: Transcription Factor

Available separately:

Standard ligation-based
library preparation:
MicroPlex Library
Preparation Kit
orRapid tagmentationbased library preparation:
TAG kit for ChIPmentation

PAGE 7

I.III Library preparation kits
Diagenode’s library preparation kits have been extensively validated with ChIP-seq samples. The MicroPlex Library Preparation Kit, whichuses a simple 3-step protocol, is an optimal choice for library preparation, especially for very low inputs of DNA down to 50 pg. Moreover, thekits are available with either single or dual index options.
MicroPlex Library Preparation Kit - Features

Available products

SampleFragmented dsDNA

Input

50 pg - 50 ng

ProtocolMicroPlex Library Preparation Kit v3 - with dual indexes
KITS*:

3 steps in one tube

Hands on time

UNIQUE DUAL INDEXES:
C05010008 - 24 UDI for MicroPlex v3- Set I /48 rxns
Template:
C05010009 - 24 UDI for MicroPlex v3- Set II /48 rxns
Fragmented

2 hours

Intermediate purification

noSequencing technology

Illumina

IndexesSingleUp to 384
samples
STEP 1 Template
preparation

Indexes

Included in the kit

Available separately

Manual protocol
Automated protocol

üC05010003 - 24 Dual indexes for MicroPlex Kit v3 /48 rxns
C05010004 - 96 Dual indexes for MicroPlex Kit v3 – Set I /96 rxns
C05010005 - 96 Dual indexes for MicroPlex Kit v3 – Set II /96 rxns
C05010006 - 96 Dual indexes for MicroPlex Kit v3 – Set III /96 rxns
C05010007 - 96 Dual indexes for MicroPlex Kit v3 – Set IV /96 rxns
5 minutes*
STEP 2 Library synthesis*The indexes for multiplexing are not included in the kits.

Dual, Unique Dual

Up to 12 samples

Stem-loop
Adaptorü
Template:

Fragmented
dsDNA/cDNA

DNA
Repairü

5 minutes*

Template:
Fragmented
dsDNA/cDNA

5’

DNA
RepairCleavable
Replication
Stop

Cleavable
Replication
Stop

5’

5’
3’ rxns
C05010012 - MicroPlex Library Preparation
Kit v2 (12 indexes) /12
Cleavable
Replication
Stop

Blunt-end Ligation
Nick

Stem-loop
Adaptor5’

5’ Nick

5 minutes*

STEP 2 Library synthesis
Stem-loop
Adaptor3’

5 minutes*

Additionof Adaptors
MicroPlex Library Preparation Kit v2
3’ - with single indexes

How the MicroPlex Library Preparation Kit Works
STEP 1 Template preparation

DNA
Repair

dsDNA/cDNA

DUAL INDEXES:®

Multiplexingü

5 minutes*

STEP 1 Template preparation

C05010001 - MicroPlex Library Preparation Kit v3 /48 rxns

5 minutes*

STEP 3 Library amplification
Extension and Cleavage

Additionof Adaptors

5’3’Blunt-end Ligation
Nick

Cleavable
Replication
Stop
Stem-loop
AdaptorBarcodePrimer A

High Fidelity Amplification

5’

BarcodePrimer B

5’ Nick* hands-on-time

5 minutes*
Microplex- protocol with dual indexes.
5 minutes*
STEP 3 Library amplification
STEP 2 workflow
Library synthesis
An input of 50 pg to 50 ng of fragmented dsDNA is converted into sequencing-ready libraries for Illumina® NGS platforms using a fast and simple 3-step protocol.
Stem-loop
Adaptor3’
5’
Cleavable
Replication
Stop

Extension and Cleavage

Additionof Adaptors

5’3’Blunt-end Ligation
Nick

5’

Cleavable
Replication
Stop
Stem-loop
AdaptorBarcodePrimer A

High Fidelity Amplificationwww.diagenode.com |BarcodePAGE 8A quick glance: ChIP kit features*H: Histones*TF: Transcription Factor

KITµChIPmentationfor Histones

ChIPmentationfor Histones

iDeal ChIP-qPCR

iDeal ChIP-seq
for Histones

iDeal ChIP-seq
for TF

True MicroChIPseq

iDeal ChIP-FFPE
Kit

Universal Plant
ChIP-seq

NGS

NGS

qPCR

qPCR, NGSqPCR, NGSqPCR, NGSqPCR, NGSqPCR, NGS

Starting material:
cells per 1 chromatinprep

No. of IP x No. of cells

700 K - 7 M

H*: 700 K - 7 M
TF*: 25 M

700 K - 7 M

25 M

No. of IP x No. of
cells

-

-

Number of cells per 1 IP

10 K - 100 K

5K-1M

H: 100 K - 1 M
TF: 4 M

100 K - 1 M

4M

10 K - 100 K--

Starting material:
tissue per 1 chromatin
prep

-

-

H: 20 mg - 30 mg
TF: 200 mg

20 mg - 30 mg

200 mg-up to 6 slides

0.1 - 2 g

Amount of tissue per 1 IP--

H: 1.5 - 5 mg
TF: 30 mg

1.5 - 5 mg

30 mg

-

up to 6 slides

0.007 - 0.13 g

Histones

Histones

Histones, TF

Histones

TF

Histones

Histones, TF

Histones

FEATURES

Downstream application

TargetIncluded buffers
DNA purification

n/a

n/a

ü

ü

ü

ü

ü

ü

Control antibodies

IgG, H3K4me3

IgG, H3K4me3-

IgG, H3K4me3

IgG, CTCF

IgG, H3K4me3-

IgG, H3K4me3

Control primers(+)GAPDH TSS, (-)
Myoglobin exon 2

Human: (+)GAPDH,(-)Myoglobin exon 2-(+)GAPDH TSS,(-)Myoglobin exon 2

Human: (+)H19,(-)Myoglobin exon 2(+)GAPDH TSS,(-)Myoglobin exon 2-

Arabidopsis: (+)FLCATG, (-)FLC-Intron1

ü

ü

n/a

Separately in MicroPlex Library Preparation Kit or TAG kit for ChIPmentation

IndexesAvailable separately

Available separatelyn/aAvailable separately

Manual Kits

C01011012 (8 rxns)
C01011011 (24 rxns)

C01011009 (24 rxns)

C01010180(24 rxns)

C01010050 (10 rxns)
C01010051 (24 rxns)
C01010059 (100 rxns)

C01010054 (10 rxns)
C01010055 (24 rxns)
C01010170 (100 rxns)

C01010132 (20 rxns)

C01010190 (24rxns)

C01010152 (24 rxns)

Automated Kits - for
IP-Star-

C01011009 (24 rxns)

C01010181(24 rxns)

C01010057 (24 rxns)
C01010171 (100 rxns)

C01010058 (24 rxns)
C01010172 (100 rxns)

C01010140 (16 rxns)-

C01010153 (24 rxns)

Compatible Chromatin
EasyShear Kit

C01020012

C01020010

C01020013

C01020010

C01020013

C01020012

C01020013

C01020014

ü

ü

ü

ü

ü

ü

ü

ü

Library prep reagents

ORDERING

Cell lysis, Chromatin shearing, Immunoprecipitation

Services

This table presents the standard quantity of cells/tissues for each kit. It is possible to scale up or scale down the quantity of the material - please refer to the corresponding manual.
Innovating Epigenetics Solutions

PAGE 9

II. Tagmentation-based technologies

Tagmentation offers numerous benefits:
9 Supports new barcoding approaches

Next generation sequencing technology in the last decade has allowed higher sample
throughput at a significantly reduced cost, necessitating the development of novel sequencing
applications and methods. In one such method, tagmentation, a modified, hyperactive
transposase (Tn5) cuts double-stranded DNA and simultaneously ligates linker sequences
to both ends in short reaction time.
The high efficiency of this approach reduces both the input required as well as hands-ontime compared to ligation-based library preparation methods.

9 Compatible with many different library
preparation methods such as ATACseq, CUT&TAG, ChIL, ChIPmentation,
TIP-seq, CHANGE-seq and others
9 Comprehensive with supporting
reagents as well as optimized andcomplete tagmentation-based
solutions complement our Tn5

Products for tagmentation•

Tagmentase (Tn5 transposase) unloaded (C01070010) – not loaded with DNA oligos, can be loaded with custom DNA oligos•

Tagmentation Dilution Buffer (C01070011) – for dilution of Diagenode Tagmentase before or after transposome assembly•

Tagmentase (Tn5 transposase) loaded (C01070012) – preloaded with Nextera sequencing adaptors compatible with Illumina
sequencing platforms•

Tagmentation Buffers – should be used in combination with Diagenode Tagmentase (Tn5 transposase) for any tagmentation reaction.
Two versions available:• (1x) (C01019042) – for low volume samples, it does not require any dilution. Application example: ChIPmentation• (2x) (C01019043) – used as half of the total volume reaction. Application example: ATAC-seq•

Primer indexes for Tagmented libraries – libraries multiplexing up to 72 samples:• 24 Single indexes for tagmented libraries (C01011032)• 24 UDI for tagmented libraries - Set I (C01011034)• 24 UDI for tagmented libraries - Set II (C01011036)• 24 UDI for tagmented libraries - Set III (C01011037)

www.diagenode.com |PAGE 10

9 Optimized protocol for cells - as little
as 50K per tagmentation reaction

II.I ATAC-seq
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) allows forassessing genome-wide chromatin accessibility. The technology is based on the use of
the transposase Tn5 which cuts exposed open chromatin and simultaneously incorporates
adapters for subsequent amplification and sequencing.
•••

Assess open regions of chromatin at single nucleotide resolution
Gain insight into gene regulation and understand open chromatin signatures
Determine nucleosome positions at single nucleotide resolution

9 Highly efficient nuclei extraction fromtissue9 Optimized library prep step to avoid
overamplification
9 Easy and efficient DNA capture after
the tagmentation reaction using
Diagenode's DiaPure columns
9 Robust protocol with highreproducibility between replicatesand repetitive experiments

Optimized solutions for ATAC-seq:•

For cells: ATAC-seq kit (C01080002) + primer indexes fortagmented libraries•

For tissue: ATAC-seq package for tissue (C01080006) complete solution including all reagentsPrimer indexes for tagmented libraries••••

24 Single indexes for tagmented libraries (C01011032)
24 UDI for tagmented libraries - Set I (C01011034)
24 UDI for tagmented libraries - Set II (C01011036)
24 UDI for tagmented libraries - Set III (C01011037)

Separately available products:
•
•
•
•
•

Tagmentase (Tn5 transposase) loaded (C01070012)
Tagmentase (Tn5 transposase) unloaded (C01070010)
Tagmentation Buffer (2x) (C01019043)
Tissue Nuclei Extraction for ATAC-seq (C01080004)
MicroChIP DiaPure columns (C03040001)

Innovating Epigenetics Solutions

Figure 1. Sequencing profiles of ATAC-seq library (3 replicates) prepared with
the Diagenode ATAC-seq kit and 24 UDI for tagmented libraries (Cat. No.
C01011034) on 50,000 nuclei from K562 cells.

ATAC-seq Workflow

STEP
1a

Day
1

2
hours

STEP
1b

Cell lysis and nuclei extraction

Day
1

4-5
hours

Tissue lysis and nuclei extraction

STEP
2
Day
1

1.5
hours

The ATAC-seq protocol consists of 3 steps: nuclei
preparation, tagmentation and library amplification.
First, the cells undergo the lysis, ending with thecrude nuclei. Then, the nuclei are incubated witha Tagmentase (Tn5 transposase), which cuts the
genomic regions associated with open chromatin andinserts the sequencing adaptors.
Finally, the generated libraries are amplified and canbe used for sequencing. High-throughput sequencing
will then detect peaks, in open regions of the chromatin
only, giving a map of the chromatin status in the wholegenome of the sample.

Tagmentation andDNA purification

STEP
3

Day
2

6
hours

Library
amplification
STEP
4

Size
selection

STEP
5

Qualitycontrol

Day
2

1.5
hours

Day
3

Sequencing

Chromatin

Tagmentase

Fragmented DNA
with adaptors

Manualprocessing

Autoprocessing

www.diagenode.com |PAGE 11

PAGE 12

II.II ChIPmentation

9 Easier and faster than classical
ChIP-seq

Diagenode’s unique ChIPmentation technology, based on tagmentation, enables theintegration of library preparation during ChIP itself using a transposase loaded withsequencing adaptors. Unlike standard library preparation techniques that require many
steps, ChIPmentation incorporates an easier and shorter protocol. Moreover, this reduced
number of steps allows successful IPs on lower amounts of chromatin, which makes it ideal
to analyze numerous histone marks on each chromatin sample.

9 One step library preparation
9 Elimination of sequencing adapter
dimers9 High quality sequencing data
9 Solution of choice for highthroughput projects

Optimized solutions for:•Low cell number - µChIPmentation for Histones (C01011011)
for as little as 10,000 cells per reaction, optimized protocol for
FACS sorted cells•

Standard cell number – ChIPmentation Kit for Histones(C01011009)•

Library preparation using tagmentation – TAG Kit for
ChIPmentation (C01011030) can be used with any ChIP protocol•

Multiplexing - Primer indexes for tagmented libraries: 24
UDI for tagmented libraries, Set I – III (C0101134, C01011036,
C01011037)

Separately available products:•

Standalone Tn5 transposase: Tagmentase loaded (C01070012)
and Tagmentase unloaded (C01070010)•

Tagmentation Buffer (1x) (C01019042)•

ChIP-seq grade antibodies

Innovating Epigenetics Solutions

Figure 2. Sequencing profiles of µChIPmentation libraries
Chromatin preparation and immunoprecipitation have been performed on 10,000
cells using the µChIPmentation Kit for Histones (Cat. No. C01011011) and 24 SI
for Tagmented libraries (Cat. No. C010111032) using K562 cells. The Diagenodeantibodies targeting H3K4me3 (Cat. No. C15410003), H3K27ac (Cat. No.
C15410196), H3K27me3 (Cat. No. C15410195) and H3K9me3 (Cat. No. C15410193)
have been used.

ChIPmentation Workflow

CHROMATIN PREPARATION

ChIPmentation
STEP
1

Cell collection andDNA-protein cross-linking
Day 1

STEP
2

Day 1

Cell lysis andchromatin shearing

STEP
3

IP & TAGMENTATION

Magnetic
immunoprecipitation

Day
1-2

Day
1-2

ChIPmentation: after cell collection, the DNA andassociated proteins are crosslinked in living cells
using formaldehyde. Then cells are lysed andchromatin is sheared by sonication (Bioruptor) toobtain the fragments between 100 – 600 bp. Crosslinked protein-chromatin complexes of interest are
selectively immunoprecipitated from the cell debris
using an appropriate protein-specific antibody.
Tagmentase loaded with sequencing adaptors is
added enabling one-step library preparation: thetagmentase
introduces
sequencing-compatible
adaptors in a single-step reaction directly on beadbound chromatin.
After stripping, end-repair and reverse cross-linking,the generated libraries can be amplified and used forsequencing.

Tagmentation:
one step adaptor insertion
into chromatin

STEP
4

LIBRARY PROCESSING

Manual Auto

Stripping, end-repair
and reverse cross-linking
Day 2

Universal Primer

STEP
5

Library amplification

Day 2

Primer Index

STEP
6Clean-up

STEP
7

Quality control

Day 3

Sequencing

Protein of interest

DNA

Magnetic bead

Tagmentation Enzyme loaded with adaptors

Other protein

Antibody

MagnetAuto processing

Manual processing

www.diagenode.com |PAGE 13

PAGE 14

II.III CUT&Tag
CUT&Tag-sequencing (Cleavage Under Targets and Tagmentation) is a new chromatin profiling method providing high quality sequencing
data from low starting amount. This alternative to ChIP-seq method, combines antibody-targeted controlled cleavage by a protein A-Tn5
fusion with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. Diagenode’s iDeal CUT&Tag kit for
Histones provides an optimized protocol for a rapid chromatin profiling on histone marks. The protocol is optimized for native cells (10,000300,000 cells per reaction) and can be completed within 2.5 days.
For a complete CUT&Tag protocol the following items must bepurchased:•

iDeal CUT&Tag for Histones C01070020 - including all reagentsfor CUT&Tag workflow (buffers, pA-Tn5, CoA beads, DNA
purification)•

Antibody package for CUT&Tag (anti-rabbit C01070022 or antimouse C01070023) - including the secondary antibody, positive
and negative control antibodies and primers•

Antibody recognizing the protein of interest – choose one of
Diagenode’s validated antibodies•

Primer indexes for tagmented libraries - for multiplexing up to 72
samples

Separately available products:•

Fusion protein – compatible with CUT&Tag, but also otherapplications like ACT-seq, CoBATCH, TIP-seq and more.
pA/Tn5 Transposase - loaded (C01070001)
pA/Tn5 Transposase - unloaded (C01070002)

Figure 3. CUT&Tag profiles show typical enrichments specific for agiven histone mark. Representative screenshots for H3K27me3 (red) andH3K4me3 (green) are shown at selected loci. H3K27me3, which marks
inactive regions (red), does not show enrichment over open chromatin
regions, marked by H3K4me3 (green). CUT&Tag was performed using
50,000 of K562 cells and Diagenode H3K4me3 polyclonal ChIP-seq antibody(Cat. No. C15410003), and H3K27me3 polyclonal ChIP-seq grade (Cat. No.
C15410195).

Innovating Epigenetics Solutions•

CUT&Tag grade antibodies•

DNA purification
IPure kit v2 (C03010014)
MicroChIP DiaPure columns (C03040001)•

Primer indexes for tagmented libraries
24 Single indexes for tagmented libraries (C01011032)
24 UDI for Tagmented libraries - Set I (C01011034)
24 UDI for Tagmented libraries - Set II (C01011036)
24 UDI for Tagmented libraries - Set III (C01011037)

CUT&Tag Workflow

in cells, on ConA magnetic beads

STEP
1

Cell preparation
and ConA beads binding

1h
Day
1

Cell permeabilizationand primary antibody

STEP
2

Over
night

STEP
3

Secondary antibody
binding

1h15

STEP
4

Targeted tagmentation

3h30

STEP
5

DNA purification

1h

STEP
6

in tubes

Library Amplification

Optional: KAPA® Library quatiﬁcation

STEP
7

Library clean-up and QC

Optional: qPCR relative enrichment

ConA beads
Cells of interest

Chromatin

Primary Antibody

pA-Tn5 Tagmentase

Protein of interest

Secondary Antibody

Pause points

Day
2

1h30

Then, Diagenode’s protein pA-Tn5 Transposase loaded is bound to the complex. Protein A guides Tn5transposase on chromatin to the antibody attached to
its target. Tn5 transposase is activated by Mg+2 ions toinsert the sequencing adaptors into genomic regionsof interest. DNA is then purified and the tagmented
genomic regions of interest are amplified by PCR using
Diagenode’s Primer Indexes for tagmented libraries.

9 Rapid and easy chromatin profilingassay for histones marks
		 - Native cells: no fixation or
chromatin fragmentation

1h

2h

The iDeal CUT&Tag protocol involves the binding ofcells on solid phase ConA magnetic beads, allowing
magnetic handling of the cells for the major steps ofthe protocol. Bead-bound cells are permeabilized andincubated with primary antibody against a target ofinterest and secondary antibody.

		 - Easy sample handling with
ConA magnetic beads
Day 3		 - Integrated library prep
9 High resolution and sensitivity
9 Low cell number required(10K – 300K)
9 Lower sequencing depth and no
input required compared to ChIP

2h30

www.diagenode.com |PAGE 15

PAGE 16

III. Antibodies
Obtaining highly sensitive and highly specific antibodies is challenging for researchers. Many antibodies that are used in experimental assays
have limited validation behind them, and the data given by the provider are not always lot-specific.
Quality matters! That is why we validate the antibodies at Diagenode.

At Diagenode we assign our R&D and production experts to continuously deliver novel antibodies of the highest quality. Diagenode’s
selection is exclusively dedicated for epigenetics research. We validate our antibodies in epigenetic applications, including ChIP, ChIP-seq
and CUT&Tag. Only the antibodies which pass the rigorous QC are released as ChIP, ChIP-seq or CUT&Tag grade. We validate each lot and
we are transparent – batch-specific validation data are available on the website. We provide the antibodies you can trust! Check out thecomplete list of antibodies on our website www.diagenode.com
ChIP validation

DIAGENODE OFFERS
A WIDE BREADTH OF
ANTIBODIES FOR:

ChIP-seq validation

CUT&Tag validation• Native and modified histones• DNA methylation• Chromatin modifying proteins• Transcription factors• RNA modifications• Nuclear receptors• CRISPR Cas9

Innovating Epigenetics Solutions

PAGE 17

Why Diagenode's antibodies?

UNMATCHED EXPERTISE

BATCH-SPECIFIC DATASTRICT QUALITY STANDARDS

with 15+ years of epigenetics-focused
antibody validation

available on the website

with rigorous QC lot-to-lot comparison

NUMEROUS VALIDATION STEPS
to guarantee results (includes peptide array
confirmation, siRNA validation, ChIP,
ChIP-seq, CUT&Tag)

www.diagenode.com |PAGE 18

Kits and reagents highlights
CHIP ON FFPE SAMPLES
iDeal ChIP-FFPE Kit
9 Fast and user-friendly deparaffinization workflow
9 Deparaffinization: less toxic than a conventional xylene-based method
9 Easy recovery of re-hydrated tissue due to DiaFilter columns
9 Fast chromatin preparation without enzymatic digestion
9 A mild de-crosslinking preserves dsDNA
9 Eluted DNA suitable for qPCR analysis or other down-stream applications

CHIP ON PLANT
Universal Plant ChIP-seq kit
9 Specifically optimized for extracting plant chromatin
9 Optimized crosslinking (crosslinking bags)
9 Compatible with low input
9 Higher enrichment
9 Higher DNA recovery after ChIP
9 Tested on many plant species (tomato, populus, Arabidposis, rice and others)
9 Validated with MicroPlex Library Preparation Kit for library prep

DNA PURIFICATION
I. The IPure kit v2 (C03010014 (24 rxns), C03010015 (100 rxns)), based on magnetic beads, is specifically
optimized for efficient DNA purification after ChIP.
9 Significantly greater yields than with column-based purification
9 Recovery of small amounts of DNA
9 Straightforward protocol using magnetic beads
9 Toxic reagents not used (e.g. phenol/chloroform)
9 Provides pure DNA for any downstream application (e. g. NGS)

Innovating Epigenetics Solutions

II. The MicroChIP DiaPure columns C03040001, is specifically optimized for efficient DNA purification of low concentrated samples.
9 Perfect for low concentrated samples (elution from 6 µl)
9 DNA recovery 70-90% (50bp - 10kB)
9 No toxic reagents (e.g. phenol/chloroform)
9 Provides pure DNA for any downstream application (e. g. NGS)

Other solutions to use with our products or your own protocols
FIXATION REAGENT FOR INDIRECT PROTEINS
For proteins not bound directly to DNA, use ChIP Cross-link Gold (Cat. No. C01019027) for efficient protein-protein fixation in higher orderor dynamic interactions.

CHIP NEGATIVE CONTROLS
Depending on the antibody of interest, choose between rabbit, mouse or rat IgG.

BEADSExtensively validated magnetic and agarose beads validated for isolation of immune complexes in ChIP experiments.
MAGNETIC RACKUse Diagenode’s DiaMag 0.2 ml, for fast and efficient isolation of magnetic beads.

PRIMER PAIRSCheck out our list of ChIP/ChIP-seq grade primer pairs on our website.

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