ChIP-IT® PBMC
(version A3)
Catalog No. 53042

Copyright 2014 Active Motif, Inc.

Please Read Before Starting:
The ChIP-IT® PBMC Kit contains an optimized protocol and buffer system
to ensure optimal enrichment of chromatin and high sensitivity ChIP.s It
is important to follow our protocol and recommendations throughout theentire manual as many steps may differ from traditional ChIP protocols.
Please pay particular attention to our notes regarding the processing of
input chromatin for agarose gel analysis prior to the chromatin immunoprecipitation reaction.

Information in this manual is subject to change without notice and does not constitute a commitment on the part of Active Motif, Inc. It is supplied on an “as is” basis without any warranty of
any kind, either explicit or implied. Information may be changed or updated in this manual at any
time.
This documentation may not be copied, transferred, reproduced, disclosed, or duplicated, inwhole or in part, without the prior written consent of Active Motif, Inc. This documentation is proprietary information and protected by the copyright laws of the United States and international
treaties.
The manufacturer of this documentation is Active Motif, Inc.
© 2014 Active Motif, Inc., 1914 Palomar Oaks Way, Suite 150; Carlsbad, CA 92008. All rights
reserved.
All trademarks, trade names, service marks or logos referenced herein belong to their respective
companies.
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TABLE OF CONTENTS

Page

Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .1
Flow Chart of Process . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
Kit Performance and Benefits . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Protocol Overview and Time Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
Kit Components and Storage
ChIP-IT PBMC Kit . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Additional Materials Required . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
Protocols – Experimental Set Up
Cell Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Buffer Preparation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
Quick Chart for Preparing Buffers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Recommendations . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Protocols – Preparation of Sheared Chromatin
Section A. Cell Fixation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
Section B. Chromatin Sonication. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Protocols – Chromatin Immunoprecipitation
Section C. Immunoprecipitation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .14
Protocols – ChIP DNA Purification
Section D. Reversal of Cross-links and DNA Purification . . . . . . . . . . . . . . . . . . . . . . . 16
Protocols – ChIP DNA Analysis
Section E. Quantitative PCR (qPCR) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .17
Section F. ChIP-Seq . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Appendix
Section G. qPCR Primer Design and Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . 20
Section H. Troubleshooting Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
Technical Services . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24

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Overview
Chromatin Immunoprecipitation (ChIP) is a powerful tool for studying protein/DNA interactions,
including transcription factors, co-regulatory proteins, modified histones, chromatin-modifying
enzymes and polymerases because it enables identification of the localization of proteins boundto specific DNA loci. When used in combination with whole-genome analysis such as ChIP-Seq or
ChIP-chip, insights are possible into gene regulation, gene expression, mechanisms of chromatin
modification and pathway analysis.
However, ChIP can be technically demanding. The method requires high-quality antibodies torecognize the fixed, target-bound proteins of interest, and an efficient means to precipitate theantibody/chromatin complex (usually protein A or G beads). In addition, specialized buffers,
inhibitor cocktails and blocking reagents are required to minimize non-specific enrichment andreduce protein degradation. The difficulties of ChIP are further compounded when working with
dificult to lyse cells, such as peripheral blood monuclear cells (PBMCs), including lymphocytes (Tcells, B cells and NK cells) and monocytes.
Active Motif’s ChIP-IT® PBMC Kit is designed to overcome these obstacles and generate highquality chromatin from PBMCs (including lymphocytes and monocytes) for analysis using thehighly sensitive, low background ChIP reagents provided in the Kit. These optimzed reagents andprotocols translate into better ChIP data.
The ChIP-IT PBMC Kit contains sufficient reagents to perform 16 chromatin preparation andimmunoprecipitation reactions. We recommend the use of Active Motif’s ChIP-IT® qPCR Analysis
Kit in combination with the ChIP-IT PBMC Kit for complete data analysis. To learn about available
ChIP-IT® Control Kits, control qPCR primer sets, ChIP-Seq validated antibodies, or Active Motif’s
EpiShear™ sonication devices, please visit our website at www.activemotif.com/chip.

product

formatcatalog no.

ChIP-IT® PBMC

16 rxns

53042

ChIP-IT® qPCR Analysis Kit

10 rxns

53029

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1Flow Chart of Process
Cross lin protein to N inliving ells it ormal e eeverse ross lin s igest
it Proteinase an N p ri
N is no rea or anal sis

Brea open ells ans ear Nsoni ationl te romatin rom
ol mn an save lo t ro ganti oprimaro interest

Capt re anti oo nprotein N omple es an assing C P iltration Col mns

Flow Chart of the ChIP-IT PBMC Assay.
In ChIP-IT PBMC, intact cells are fixed with formaldehyde, which cross-links and preserves protein/DNA interactions. DNA isthen sheared into small fragments using sonication and incubated with an antibody directed against the DNA-binding protein
of interest. The antibody-bound protein/DNA complexes are immunoprecipitated through the use of Protein G agarose beads
and washed via gravity filtration. Following immunoprecipitation, cross-links are reversed, the proteins are removed by Proteinase K, and the DNA is recovered and purified. ChIP enriched DNA can be used for either gene-specific or whole-genome
analysis.

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2

Kit Performance and Benefits
ChIP-IT PBMC Advantages:• Optimized buffers improve cell lysis and chromatin yields when working with PBMCs (including T cells, B cells, NK cells and monocytes)• Highly sensitive DNA enrichment due to the inclusion of an antibody blocker which reduces
background levels caused by non-specific binding events• Filtration based washes are the easiest wash method available and result in increased
consistency in multi-sample experiments• Highly robust procedure has been validated in both qPCR and ChIP-Seq analysis

Binding events detected per 1000 cells

100
90
80
70
60

H3K4me3 ChIP on PBMCs
PBMC Sample 1
PBMC Sample 2
PBMC Sample 3

50
40
30
20
10
0

Negative Control
Primer Set 2

Positive Control Primer

Figure 1: Immunoprecipitation sensitivity of ChIP-IT High Sensitivity Kit.
PBMC chromatin was prepared according to the manual using 20 million PBMC cells per reaction. ChIP was performed using
the Histone H3K4me3 antibody on 10 µg of chromatin. Following enrichment, qPCR was performed using the ChIP-IT qPCR
Analysis Kit (Catalog No. 53029) to normalize the data. The negative control primer set (Catalog No. 71002) showed no enrichment, while the positive control primer sets showed nice enrichment of H3K4m3 in the three PBMC samples tested. The
data represents triplicate values expressed as Binding events detected per 1,000 cells. To convert this scale to the percent of
ChIP input recovered, divide the values by 1,000.

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3

H3K c ChIP on C

cells

Binding events detected per 1000 cells

600
500

ell pop lation 1
ell pop lation 2

400
300
200
100
0

Negative Primer
Set 1

Positive Primer Set
C B2

Positive Primer Set
P 2

Figure 2: ChIP-IT PBMC on CD8+ selected T cells.
T cell chromatin was prepared according to the manual using 20 million CD8+ sorted T cells per reaction. ChIP was
performed using the Histone H3K9ac antibody on 10 µg of chromatin. Following enrichment, qPCR was performed using the
ChIP-IT qPCR Analysis Kit (Catalog No. 53029) to normalize the data. The negative control primer set (Catalog No. 71001)
showed no enrichment, while both the ACTB-2 (Catalog No. 71005) and GAPDH-2 (Catalog No. 71006) positive control primer
sets showed nice enrichment of H3K9ac in the two T cell populations tested. The data represents triplicate values expressed
as Binding events detected per 1,000 cells. To convert this scale to the percent of ChIP input recovered, divide the values by
1,000.

Protocol Overview and Time Table
Required Time
Cell Fixation and Lysis

2 hours

Chromatin Sonication

40 minutes per sample

Assessment of Chromatin Size

Overnight incubation

Immunoprecipitation

Overnight incubation

Binding to Protein G agarose Beads

3 hours

Wash Immune Complexes

20 minutes

Reversal of Cross-links

2.5 hours

DNA Purification

15 minutes

qPCR Analysis

2 hourswww.activemotif.com

4Kit Components and Storage
Please store each component at the temperature indicated in the table below. Do not re-freeze
the Protein G Agarose Beads. Once thawed, Protein G beads should be stored at 4°C.
Reagents

Quantity

Storage

RNase A (10 µg/µl)

40 µl

-20°C

Proteinase K (10 µg/µl)

200 µl-20°C

Blocker

100 µl-20°C

100 mM PMSF

500 µl-20°C

Protease Inhibitor Cocktail (PIC)

500 µl-20°C

Precipitation Buffer

1.5 ml-20°C

Carrier

35 µl

-20°C

10X PBS

120 ml-20°C

Protein G Agarose Beads*

500 µl4°C

Swelling Buffer

100 ml4°C

TE pH 8.0

3 x 1.5 ml

RTDetergent

25 ml

RT

Stop Solution

20 ml

RT

5 M NaCl

400 µlRT

ChIP Filtration Columns

16 ea

RT

ChIP Buffer

35 ml

RT

Wash Buffer AM1

100 mlRT

Elution Buffer AM4

2 x 1.5 ml

RT

DNA Purification Binding Buffer

50 ml

RT

3 M Sodium Acetate

500 µlRT

DNA Purification Wash Buffer**

10 ml

RT

DNA Purification Elution Buffer

5 ml

RT

DNA Purification Columns

16 ea

RT

* The Protein G Agarose Beads are shipped on dry ice and can be stored frozen until their firstuse. Once thawed, the Protein G beads should not be re-frozen by the customer. Protein G
Agarose Beads should be stored at 4ºC.
**Requires the addition of ethanol before use.

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5Additional materials required• A ChIP-validated antibody directed against the protein of interest• 37% formaldehyde solution with 10-15% methyl alcohol to prevent polymerization. Do not
use paraformaldehyde• 100% ethanol (absolute)• 70% ethanol• DNase-free H2O• Centrifuge• 15 and 50 ml conical tubes• Metal spatula• Dry ice for flash freezing• Apparatus to rotate tubes end-to-end at 4°C (e.g. a Labquake from Barnstead/Thermolyne
with a tube holder for 1.5 ml microcentrifuge tubes or Glas-Col, Catalog No. 099A RD4512)• Microcentrifuge (table top centrifuge 4°C) and microcentrifuge tubes• 250 µl PCR tubes• Thermocycler• Phenol• Chloroform/isoamyl alcohol (24:1)• Spectrophotometer for DNA quantitation• Pipettors and tips (filter tips are recommended)• Sonicator (e.g. Active Motif’s EpiShear™ Sonicator with a 1/8” probe (Catalog No. 53051) with
the EpiShear™ Cooled Sonication Platform (Catalog No. 53080))• Agarose gel electrophoresis apparatus• (Optional) ChIP-IT® qPCR Analysis Kit (Catalog No. 53029)• (Optional) Gene-specific qPCR primer pairs for enrichment analysis; see Appendix Section I• (Optional) SYBR Green qPCR master mix (Bio-Rad Catalog No. 170-8882)

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6

Protocols – Experimental Set Up
PLEASE READ THE ENTIRE PROTOCOL BEFORE STARTING!
Cell Recommendations
When planning an experiment, calculate the number of chromatin preparations you will requireand determine the number of ChIP reactions you plan to perform on each chromatin preparation.
Be sure to include the appropriate positive and negative control ChIP reactions in your calculations. Also, note that if you wish to analyze the effect of particular compounds on protein/DNA
interactions, you should prepare chromatin from control (untreated) cells as a reference sample.
PBMCs (including lymphocytes and monocytes) are difficult to lyse cells and as a result will yieldapproximately 30-50% as compared to cell lines. The minimum recommended number of cells
that should be used for the preparation of chromatin is 10 million cells.

Buffer Preparation
A Quick Chart for preparing the buffers needed for Section A: Cell Fixation is provided on page 8.
Please refer to the descriptions below for complete details on buffer preparations.
Fixation Solution
Fixation solution should be prepared fresh before each experiment. For each cell pellet, prepare
5 ml of Fixation Solution by adding 0.5 ml 10X PBS to 4.36 ml sterile water in a 15 ml conical tube.
Using appropriate precautions (i.e. safety glasses, gloves and lab coat), add 140 µl 37% formaldehyde to the tube and vortex to mix.
Stop Solution
Is provided ready to use. Use 250 µl per 5 ml Fixation Solution.
100 mM PMSF and Protease Inhibitor Cocktail (PIC)
Thaw the PMSF and the PIC at room temperature until fully dissolved (approximately 30 minutes).
Vortex gently and spin down briefly before use, then add to the buffers immediately before use.
Detergent
Is supplied ready to use.
PBS Wash Buffer
Prepare 10 ml PBS Wash Buffer for every sample. To a 15 ml conical tube add 8.5 ml sterile water,
1 ml 10X PBS, 0.5 ml Detergent and 20 µl 100 mM PMSF. Mix by inverting. Place PBS Wash Buffer on ice to chill. PBS Wash Buffer can be prepared in large quantities and stored at 4ºC for 6
months.
Swelling Buffer
Is supplied ready to use.
ChIP Buffer
Is supplied ready to use.
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7

DNA Purification Wash Buffer
The DNA Purification Wash Buffer requires the addition of ethanol before use. The final concentration of ethanol should be 80%. Add 40 ml of fresh 100% ethanol to the DNA Purification Wash
Buffer bottle. Invert repeatedly. The buffer can be stored at room temperature after the additionof ethanol. The ethanol only needs to be added before the first use, after that the Wash Buffer isready for use.
3M Sodium Acetate
It is important to check the sodium acetate before use to ensure that the salts have notprecipitated out of solution. Once the sodium acetate is in solution it should be stored at room
temperature.
Protein G Agarose Beads
The supplied agarose beads require washing prior to use. Follow the instructions in the manual
to wash the beads for use in the ChIP reactions. There is no need to pre-block the beads or
pre-clear the sample. For best results, gently shake and invert the tube to resuspend the agarose
beads. The beads settle quickly, and therefore should be resuspended just before pipetting. We
recommend cutting 2 mm from the end of a pipet tip prior to pipetting to prevent the tip frombecoming clogged. Protein G Agarose Beads are shipped on dry ice and can be stored frozen
until their first use. Once thawed, beads should not be re-frozen by the customer. Protein G
Agarose Beads should be stored at 4ºC.

Quick Chart for Preparing Buffers for Section A: Cell Fixation
Reagents to prepare

Components

Per cell pellet

4 cell pellets

Fixation Solution

Sterile H20
10X PBS
37% Formaldehyde
TOTAL REQUIRED

4.36 ml
0.5 ml140 µl5 ml

17.44 ml
2 ml
560 µl20 ml

Stop Solution

TOTAL REQUIRED

250 µl

1 ml

PBS Wash Buffer

Sterile H20
10X PBS
Detergent
100 mM PMSFTOTAL REQUIRED

8.5 ml1 ml
0.5 ml
20 µl
10 ml

34 ml
4 ml
2 ml
80 µl
40 ml

Swelling Buffer

Swelling Buffer
Protease Inhibitor Cocktail
100 mM PMSFTOTAL REQUIRED

5 ml
5 µl
5 µl
5 ml

20 ml
20 µl
20 µl
20 ml

Detergent

TOTAL REQUIRED

375 µl

1.5 mlChIP Buffer

ChIP Buffer
Protease Inhibitor Cocktail
100 mM PMSFTOTAL REQUIRED

500 µl5 µl
5 µl
510 µl

2 ml
20 µl
20 µl
2 ml

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8

Recommendations
ChIP-validated Antibody
We recommend using 4 µg antibody per ChIP reaction in a maximum volume of 30 µl. However,this will vary according to the affinity of the antibody and the quality of the chromatin; you may
need to use more of a particular antibody. ChIP antibodies must recognize fixed, native proteinthat is bound to DNA and/or complexed with other proteins. Many antibodies that perform wellin other applications do not perform in ChIP. Thus, ChIP performed with an antibody that has notbeen ChIP-validated must include appropriate controls (such as Active Motif’s ChIP-IT Control
qPCR Kits, Catalog Nos. 53026, 53027 and 53028) to validate the chromatin preparation and theChIP methodology. To see a list of available ChIP-validated antibodies available from Active Motif,
please visit www.activemotif.com/chipabs.
Chromatin Shearing Tips
We suggest using a probe sonicator (i.e. Active Motif’s EpiShear Probe Sonicator) which employs
a direct sonication method to prepare chromatin for use in the ChIP-IT PBMC Kit. Indirect sonication systems may require longer sonication times to achieve optimal chromatin shearing. ChIP
experiments usually require chromatin that has been sheared to a size of 200-1200 bp. In general,
shearing efficiency is improved through the use of a small shearing volume and a V-bottom tube
rather than a round-bottom tube. Also, note that shearing is inefficient if the chromatin sample
becomes emulsified with air bubbles. To determine the appropriate shearing level for your sample,
set up a “practice” tube containing only ChIP Buffer. Slowly increase the sonication amplitude until
foaming starts to occur. Reduce the amplitude setting down slightly and mark this as the highest
possible intensity to use without foaming. If a chromatin preparation becomes emulsified inadvertently, discontinue shearing and centrifuge the sample at maximum speed for 4 minutes at 4ºC ina microcentrifuge to remove trapped air. Finally, to prevent overheating and denaturation of chromatin, samples should be kept on ice as much as possible during shearing, and shearing should be
performed discontinuously (i.e. sonicate for 20 seconds, then place on ice/water for 30 seconds,
sonicate again for 20 seconds, etc.). If possible, shear while on ice or use Active Motif’s EpiShear™
Cooled Sonication Platform (Catalog No. 53080) to help regulate sample temperature.
Chromatin Quantity
It is recommended to use 10-30 µg chromatin per IP reaction. However, if chromatin is in limited
supply lower amounts may be used due to the high quality of the DNA obtained from the ChIP-IT
PBMC Kit. If ChIP-Seq will be performed following enrichment, please read the recommendations
listed in Section F prior to starting the protocol.
Safety Precautions
Formaldehyde and PMSF are highly toxic chemicals. Appropriate safety precautions (i.e. safety
glasses, gloves and lab coat) should be used. Also, formaldehyde is highly toxic by inhalation andshould be used only in a ventilated hood. Finally, chromatin sonication should be performed in abiosafety hood if the chromatin is extracted from biohazardous or infectious materials.

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9

Protocols – Preparation of Sheared Chromatin
Section A: Cell Fixation
We recommend using a minimum of 10 million cells for the preparation of chromatin.
1.

Collect your PBMCs, T cells, B cells, NK cells or moncytes according to your preferred
protocol. Transfer the appropriate number of cells required for each chromatin preparation
into a conical tube and centrifuge at 1,250 x g at 4°C to collect the cells. If there are cells
that are floating or are stuck to the sides of the tube following the spin, use a metal spatula
to scrape the cells down into solution and repeat the centrifugation at 1,250 x g at 4°C for 5
minutes. Continue to repeat the scraping and spin as many times as needed to pellet all thecells. Remove and discard supernatant.
Note:

PBMCs may stick to certain plastics. Therefore, it is recommended to use a
metal spatula for cell scraping to avoid losing any sample material.

2.

Flash freeze the cell pellet(s) by imersing conical tube into dry ice. Incubate on dry ice for 10
minutes. Cell pellets may be stored at -80°C at this stage, or proceed with the next step.

3.

Prepare fresh Fixation Solution. To fix cells, add 5 ml of freshly prepared Fixative Solution to
the cell pellet and resuspend cells by pipetting up and down. Incubate at room temperaturefor 15 minutes on a roller.

4.

Stop the fixation reaction by adding 250 µl Stop Solution to the existing fixation solution.
Swirl to mix and incubate at room temperature for 5 minutes on a roller.

5.

Following the incubation, add 250 µl Detergent to each conical tube. Invert to mix. Pellet
the cells by centrifugation for 5 minutes at 1,250 x g at 4°C.

6.

If there are cells that are floating or are stuck to the sides of the tube following the spin, use
a metal spatula to scrape the cells down into solution and repeat the centrifugation at
1,250 x g at 4°C for 5 minutes. Continue to repeat the scraping and spin as many times asneeded to pellet all the cells.

7.

Remove the supernatant and discard. Resuspend the pellet(s) in 5 ml ice-cold PBS Wash
Buffer by pipetting up and down. Keep samples ice-cold for the remainder of the procedure.

8.

Centrifuge for 5 minutes at 3,200 x g at 4°C. The cell pellet will tend to be loose, so carefully remove the supernatant and discard taking care to avoid disturbing the pellet. Wash
the pellet(s) a second time in 5 ml ice-cold PBS Wash Buffer by pipetting up and down.
Centrifuge for 5 minutes at 3,200 x g at 4°C. Carefully remove the supernatant and discard.

9.

Flash freeze the cell pellet(s) by imersing conical tube into dry ice. The freeze/thaw will tohelp facilitate cell lysis. Incubate on dry ice for 10 minutes. Cell pellets may be stored at-80°C at this stage, or proceed with the next step.

10. Resuspend each pellet(s) in 5 ml ice-cold Swelling Buffer supplemented with 5 µl PIC and5 µl 100 mM PMSF. Pipet up and down to mix.
11.

Incubate on ice for 30 minutes.

12. Add 125 µl Detergent to each cell pellet. Vortex for 30 sec on highest setting to lyse thecells.
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10Note:

We do not recommend the use of a dounce homogenizer to assist in cell lysis
as the transfer process to and from the dounce increases sample loss. If cells
continue to have difficulty lysing, we suggest additional sonication.

13. Centrifuge for 10 minutes at 3,200 x g at 4°C. Remove and discard the supernatant.
14. Resuspend each pellet in 500 µl ChIP Buffer supplemented with 5 µl PIC and 5 µl 100 mM
PMSF. Transfer the contents to a new 2 ml microcentrifuge tube.
15. Incubate on ice for 10 minutes. Proceed to Step B: Chromatin Sonication.

Section B. Chromatin Sonication
The section below describes the fragmentation of chromatin using sonication. Sonication results
may vary depending on cell type and sonication device being used. This protocol has been validated using Active Motif’s EpiShear™ Probe Sonicator in combination with an EpiShear™ Cooled
Sonication Platform to maintain probe height and temperature consistency between samples. We
do not recommend sonication of samples containing less than 1 x 107 cells and/or 350 µl volume.
The ChIP Buffer has been optimized for immunoprecipitation performance, however, due to its
unique composition optimization of sonication conditions may be required. To maintain the highsensitivity of the assay, we recommend using our buffer system and altering the sonication time
and/or amplitude of your sonication system to achieve the desired fragmentation (e.g. somesystems may require as much as a three-fold increase in sonication time to improve chromatin
shearing). Please pay particular attention to our protocol regarding the processing of input chromatin for agarose gel analysis prior to the chromatin immunoprecipitation reaction as many steps
may differ from traditional ChIP protocols and failure to follow the outlined procedure may leadto artifacts in the gel images as shown in Figure 3 on page 13.
1.

Place the 2 ml microcentrifuge tube containing the chromatin into the tube cooler or packed
ice. Open cap and submerge the microtip into the liquid until the microtip is approximately
5 mm from the bottom of the tube. Sonicate according to optimized settings for the cell typebeing used (see Recommendations on page 9). A recommended starting range for PBMCs
is: 4 rounds of sonication at 42% amplitude, pulse for 30 seconds on and 30 seconds off
for a total sonication “on” time of 5 minutes per round. (Total sonication “on” time is 20
minutes and total elapsed time is 40 minutes per sample.)2.

Spin tubes at 4°C in a microcentrifuge at maximum speed for 5 minutes to pellet the cellulardebris.

3.

Transfer 25 µl of each chromatin preparation into a 250 µl PCR tube for analysis of shearing
efficiency and chromatin quantification. This sample will be used to generate the Input DNA.

4.

Aliquot the remainder of each chromatin preparation into 1.5 ml microcentrifuge tubes. We
recommend making aliquots of 250 µl volume.

5.

Flash freeze the chromatin by imersing tubes into dry ice for 10 minutes and store at -80°C.
Note:

The size of the chromatin sonication should be verified before proceeding to
the immunoprecipitation step.

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11Input Preparation
6. To each 25 µl chromatin preparation from Step 5 above, add 175 µl TE pH 8.0 and
2 µl RNAse A. Cap the PCR tubes and vortex to mix.
7.

Incubate in a thermocycler at 37°C for 1 hour.

8.

Add 5 µl Proteinase K to each tube, vortex and incubate in a thermocycler at 37°C for 3
hours.

9.

Add 10 µl 5 M NaCl, vortex and incubate at 65°C for 6-16 hours to reverse cross-links.

10. Remove tubes from the thermocycler and add 250 µl phenol and 125 µl chloroform:isoamyl
alcohol (24:1). Vortex vigorously and spin tubes in a room temperature microcentrifuge at
maximum speed for 2 minutes.
11.

Transfer each upper aqueous layer to a new 1.5 ml microcentrifuge tube and add 250 µl
chloroform:isoamyl alcohol (24:1). Vortex vigorously and spin tubes in a room temperature
microcentrifuge at maximum speed for 2 minutes.

12. Transfer the upper aqueous layer to a new 1.5 ml microcentrifuge tube. Add 83 µl Precipitation Buffer, 2 µl Carrier and 900 µl absolute ethanol. Vortex to mix and chill at -80°C for
30 minutes to overnight.
13. Spin at 4°C in a microcentrifuge at maximum speed for 15 minutes.
14. Carefully remove the supernatant taking care not to disturb the pellet. Wash the pellet with
500 µl 70% ethanol and spin at 4°C in a microcentrifuge at maximum speed for 5 minutes.
15. Carefully remove the supernatant taking care not to disturb the pellet. Remove residual
ethanol with a pipet tip. Leave the tubes uncapped and air dry for 10-15 minutes.
16. When the pellets are dry, add 25 µl DNA Purification Elution Buffer to each tube. Incubate atroom temperature for 10 minutes. Then vortex to ensure the pellet is completely resuspended. This solution contains your Input DNA.
17.

Read the absorbance of each sample on a NanoDrop or other spectrophotometer at
260 nm to determine the DNA concentration of each chromatin preparation. Set aside
500 ng of DNA for analysis as described in Step 18. Store the remaining Input DNA at -20°C.

18. Analyze each chromatin preparation on an agarose gel by following the instructions below.
a.

Prepare 500 mM NaCl by adding 2 µl 5M NaCl to 18 µl sterile water. Vortex to mix.

b.

Transfer 500 ng of Input DNA to a 250 µl PCR tube and add 1 µl 500 mM NaCl. Adjust
the final volume to between 10 µl with sterile water if needed.

c.

Heat samples in a thermocycler at 100°C for 20 minutes followed by ramping thetemperature down to 50°C.

d.

Remove tubes from the thermocycler and incubate at room temperature for 5 minutes.

e.

Add gel loading buffer to each sample and run on a 1.5% agarose gel. Include 100 bp
and 1 kb DNA ladders to analyze chromatin size. DNA should appear as a smear anywhere between 200-1200 bp.

19. If chromatin preparations were successful, the aliquots stored at -80°C from Section B, Step
5 can be used to perform the ChIP reactions in Section C.
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12

Figure 3: Validation of chromatin shearing efficiency following reversal of cross-links overnight at 65°C.
Chromatin preparations of MCF-7 cells were fixed and sonicated using the EpiShear™ Probe Sonicator and EpiShear™ Cooled
Sonication Platform from Active Motif. Input DNA was prepared in duplicate according to Section B, Steps 6-17 in the manual.
In Sample 1, Step 18 was not performed and 500 ng of input DNA was loaded directly onto a 1.5% agarose gel without receiving the addition of NaCl and incubation at 100°C. The omission of Step 18 has caused a buffer artifact that makes the DNA
appear larger on a gel. The duplicate sample, Sample 2, was processed according to the manual instructions and included
the addition of NaCl and incubation at 100°C as stated in Step 18. Analysis of 500 ng of this input DNA on a 1.5% agarose
gel shows the expected fragmentation between 200-1200 bp. The difference in DNA sizing on the gel between the two
samples illustrates the importance of following the protocol recommendations regarding the processing of input chromatin
for agarose gel analysis prior to chromatin immunoprecipitation. Omission of key steps can lead to inaccurate analysis ofchromatin shearing efficiency. If the protocol steps were followed and the DNA fragments fall outside of the recommended
range, sonication conditions should be further optimized.

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Protocols – Chromatin Immunoprecipitation
Section C. Immunoprecipitation
Successful chromatin immunoprecipitation depends on the quality of the ChIP antibody and theabundance of the target protein. We recommend using 10 – 30 µg chromatin per IP reaction,although less can be used if chromatin yields are limiting.
1.

Thaw sonicated chromatin on ice. Spin chromatin at 4°C in a microcentrifuge at maximum
speed for 2 minutes.

2.

Set up the ChIP reactions by adding the components in the order shown in Table 1 below
to 1.5 ml microcentrifuge tubes. Be sure to use the DNA concentration that was determinedfor your sonicated chromatin sample to calculate the volume to use.

3.

In a 1.5 ml microcentrifuge tube prepare the antibodies to be used in the ChIP reactions.
Use a separate tube for each antibody. To the tube add 5 µl Blocker and 4 µg ChIP antibody.
(Antibody volume should not exceed 30 µl per reaction). Incubate Antibody/Blocker mix for 1
minute at room temperature and then add to the ChIP reactions.
Table 1

Reagent

1 reaction

Sheared Chromatin (10 - 30 µg)

X µl

ChIP Buffer

adjust up to 200 µl

Protease Inhibitor Cocktail (PIC)

5 µl

Antibody/Blocker mix (from Step 3)

not to exceed 35 µl

Maximum Volume Allowed

240 µlNote:

If your chromatin is too dilute to use within a 200 µl volume, we suggest preparing two immunoprecipitation reactions each using 200 µl sheared chromatin
and then pooling the IP reactions together when loading sample onto the ChIP
filtration column in Section C, Step 11.

4.

Cap tubes and incubate on an end-to-end rotator overnight at 4°C.

5.

The Protein G agarose beads require washing before use. Transfer 30 µl Protein G agarose
beads for each IP reaction to a 1.5 ml microcentrifuge tube. Add an equal volume of TE,
pH 8.0 and invert to mix. Spin at 1250 x g in a microcentrifuge for 1 minute. Remove thesupernatant equivalent to the volume of TE added to the agarose beads.
Note:

6.

Before pipetting the Protein G agarose beads, they should be fully resuspended
by inverting the tube. When pipetting the beads, cut 2 mm from the end of apipet tip to prevent the tip from becoming clogged.

Wash the beads a second time with the same volume of TE, pH 8.0. Invert to mix. Spin
at 1250 x g for 1 minute in a microcentrifuge. Remove the supernatant equivalent to thevolume of TE added to the agarose beads. The beads are now ready to use.
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7.

Spin the ChIP reactions at 1250 x g for 1 minute to collect liquid from the inside of the cap.

8.

Using a cut pipet tip, add 30 µl washed Protein G agarose beads to each immunoprecipitation reaction. Cap tubes and incubate on an end-to-end rotator at 4°C for 3 hours.

9.

Label a ChIP Filtration Column for each ChIP reaction. Remove the tab from the bottom of
the column and place in an empty 1 ml pipet tip box as a holder (see Figure 4 below).

10. Remove ChIP reactions from rotator and spin at 1250 x g for 1 minute to collect liquid frominside of the cap.
11.

Add 600 µl ChIP Buffer to each ChIP reaction then transfer the entire reaction (including theprotein G agarose beads) to its labeled column. Allow flow-through to occur by gravity.

12. During the gravity flow, transfer 100 µl per ChIP reaction of Elution Buffer AM4 to a 1.5 ml
microcentrifuge tube and allow to pre-warm at 37°C during the wash steps.
13. Wash each column with 900 µl Wash Buffer AM1. Let stand for 3 min.
14. Repeat Step 13 four more times for a total of five washes.
15. Transfer columns to a new 1.5 ml microcentrifuge tube and spin in a room temperature
microcentrifuge at 1250 x g for 3 minutes to remove residual Wash Buffer.
16. Following the spin, transfer the ChIP Filtration Columns to new 1.5 ml microcentrifuge tubes.
Add 50 µl 37°C Elution Buffer AM4 to each column. Incubate at room temperature for5 minutes. Spin in a room temperature microcentrifuge at 1250 x g for 3 minutes.
17.

With columns remaining in the same microcentrifuge tube, add another 50 µl 37°C Elution
Buffer AM4 to each column. Incubate at room temperature for 5 minutes and spin in a room
temperature microcentrifuge at 1250 x g for 3 minutes.

18. Discard the ChIP Filtration Columns. The flow-through (~100 µl volume) contains the ChIP
DNA. Proceed to Section D: DNA purification.

Figure 4: Using the ChIP Filtration Columns.
Remove the tab from the bottom of the ChIP Filtration Columns and place columns in an empty 1 ml pipet tip box to performthe wash steps.

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Protocols – ChIP DNA Purification
Section D. Reversal of Cross-links and DNA Purification
1.

Transfer each eluted ChIP DNA to a 250 µl PCR tube and add 2 µl Proteinase K. Vortex tomix and heat in a thermocycler at 55°C for 30 minutes and then increase the temperature to
80°C for 2 hours.

2.

Transfer the DNA to a 1.5 ml microcentrifuge tube and add 5 volumes (500 µl) DNA Purification Binding Buffer to each tube and vortex to mix. Adjust the pH with 5 µl 3M Sodium
Acetate. The sample should be bright yellow in color to indicate a proper pH. If your sample
is not bright yellow, please refer to the Troubleshooting guide in the Appendix for details toadjust pH prior to loading the sample into the purification column.

3.

For each sample, place a DNA purification column (AM #103928) in the collection tube andadd each pH adjusted sample to its own column. Close the cap on each column, place themwith the collection tubes in a microcentrifuge and spin them at 14,000 rpm for 1 minute.

4.

Remove the column from the collection tube, then remove and discard the flow throughfrom the collection tube. Return the column to the collection tube.

5.

Prepare DNA Purification Wash Buffer (AM #103497) before the first use. Follow the instruction on page 8 for the addition of ethanol prior to using the solution. Add 750 µl DNA
Purification Wash Buffer to each column and cap the column.

6.

Spin at 14,000 rpm for 1 minute in a microcentrifuge.

7.

Remove the column from the collection tube, then remove and discard the flow throughfrom the collection tube. Return the column to the collection tube.

8.

With the column cap open, spin at 14,000 rpm for 2 minutes in a microcentrifuge to remove
any residual Wash Buffer from the column.

9.

Transfer the column to a clean microcentrifuge tube. Depending on the method to be used
for downstream analysis of the ChIP enriched DNA, use the appropriate elution volume. For
ChIP-Seq or ChIP-chip applications, we recommend pre-warming the required elution buffer
volume at 37°C for 5 minutes prior to use.
a.

For qPCR analysis: add 100 µl of DNA Purification Elution Buffer (AM #103498) to thecenter of the column matrix and incubate for 1 minute at room temperature. Spin at
14,000 rpm for 1 minute in a microcentrifuge. Add an additional 100 µl DNA Purification
Elution Buffer to the column and incubate for 1 minute at room temperature. Spin at
14,000 rpm for 1 minute in a microcentrifuge. Total elution volume is 200 µl.

b.

For ChIP-Seq or ChIP-chip analysis: add 36 µl of 37°C DNA Purification Elution Buffer(AM #103498) to the center of the column matrix and incubate for 1 minute at room
temperature. Spin at 14,000 rpm for 1 minute in a microcentrifuge.

10. Discard column. Purified DNA may be stored at -20°C for future use.

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Protocols – ChIP DNA Analysis
Section E. Quantitative PCR (qPCR)
ChIP DNA can be analyzed on a gene-specific basis using quantitative PCR (qPCR). Positive
control and negative control PCR primer pairs should be included in every analysis to determine
the fold enrichment. Negative control primers will amplify a region of the genome not bound by
the antibody target of interest. Active Motif recommends the use of its ChIP-IT® qPCR Analysis
Kit (Catalog No. 53029) for the analysis of qPCR data. The ChIP-IT qPCR Analysis Kit contains
positive and negative control primer pairs, standard curve DNA, standard curve primers and aqPCR Analysis spreadsheet to perform the analysis calculations. Active Motif’s analysis strategy
determines primer efficiencies and the ChIP sample values are normalized according to input,
primer efficiency, chromatin amount used in the ChIP reaction and resuspension volume. The
ChIP-IT qPCR Analysis Kit provides consistency in data analysis and allows direct comparison
across samples and experiments. If not using the ChIP-IT qPCR Analysis Kit, qPCR data normalization and graphing can be done using the methods described in Section I.
1.

Below is an example qPCR reaction. Please follow the specific instructions for your qPCR
instrument. We recommend using a commercially available SYBR Green qPCR master mix(e.g. Bio-Rad Cat # 170-8882) and preparing triplicate reactions.
Reagent

20 µl PCR reactions

2X SYBR Green master mix

10 µl

Primer mix (2.5 µM each primer)*

4 µl

Sterile water

1 µl

DNA sample (ChIP or Input)

5 µl

Total volume

20 µl* We recommend designing primers to perform at an annealing temperature of 58°C so thatall qPCR reactions can be performed under identical conditions. An amplicon length of
75-150 bp is recommended. Active Motif offers validated species-specific qPCR primers
designed according to these recommendations at www.activemotif.com/chipprimers.
2.

Place tubes in a real time PCR instrument and program as below:
95°C for 2 minutes(95°C for 15 seconds, 58°C for 20 seconds, 72°C for 20 seconds) for 40 cycles

3.

If using the ChIP-IT qPCR Analysis Kit, please refer to the product manual for analysis
instructions. Otherwise, follow the recommendations in Section G.
Notes:The polymerase chain reaction (PCR) process for amplifying nucleic acid iscovered by U.S. Patent Nos. 4,683,195 and 4,683,202 assigned to Hoffmann-La
Roche. Patents pending in other countries.

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17Section F. ChIP-Seq
The ChIP-IT PBMC Kit has been extensively validated for whole genome analysis using ChIPSeq. This process involves the preparation of libraries from ChIP DNA by the addition of adapter
sequences to the ends of the DNA fragments. The library is then PCR amplified and validated
prior to sequencing.
Commercial kits are available to prepare the ChIP DNA libraries for sequencing such as Illumina®
ChIP-Seq DNA Sample Prep Kit (Catalog No. IP-102-1001) which is compatible with sequencing on
HiSeq 2000, HiSeq 1000, HiScanSQ or Genome Analyzer. For alternative sequencing platforms,
please select an appropriate library preparation method compatible with the sequencing apparatus to be used.
A. General Recommendations• We recommend using 30 µg chromatin for the ChIP Reactions, although less may be used if
chromatin amounts are limiting or you are enriching for a highly abundant histone protein• Library generation usually requires 10 ng of ChIP enriched DNA. However, by using the
ChIP-IT PBMC Kit the enriched DNA is of such a high quality that lower amounts can beused.
(See B. ChIP-Seq Requirements below for more details)• Sequence library yields should be in the range of 1-2 micrograms• 30 million sequencing reads is sufficient for most transcription factor and histone modifications• 50 bp single end reads are sufficient for unique mapping and good ChIP-Seq data, although
longer reads can be used
• Input DNA should be sequenced as a control reaction in order to identify false “peaks”
and also to reveal regions of the genome that have been duplicated. Subtracting the input
peaks from the experimental peaks will help to eliminate false data. Use 50 ng Input DNA(from Section B Step 17) for library generation.
B. ChIP-Seq Requirements
It is commonly recommended that library generation of ChIP DNA requires 10 ng of ChIP enriched
DNA. Obtaining 10 ng of ChIP DNA should be attainable when using good antibodies against
abundant histone modifications. However, 10 ng is an unrealistic number for a sequence specific
DNA binding transcription factor. Using the ChIP-IT PBMC Kit, we have routinely generated
high quality libraries from sub-nanogram levels of ChIP DNA due to the high quality of the DNA
obtained. For good ChIP-Seq data, quality enrichments with low background is more important
than the total quantity of DNA recovered. Therefore, we recommend performing qPCR on known
binding sites to verify enrichment levels against a negative control primer set using Active Motif’s
ChIP-IT qPCR Analysis Kit (Catalog No. 53029) to confirm DNA quality rather than quantifying theDNA.

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C. qPCR prior to ChIP-Seq
To perform qPCR for verification of the quality of the enriched ChIP DNA, follow the instructions
for qPCR in Section E with the following modification. The ChIP DNA will need to be diluted prior
to use in qPCR due to the reduced elution volume. Dilute 6 µl of ChIP DNA in 94 µl DNA Purification Elution Buffer (AM #103498). Use 5 µl of the diluted ChIP DNA per qPCR reaction.

Binding events detected 1 000 cells

Binding events detected 1 000 cells

Quality DNA that is suitable for use in ChIP-Seq should show enrichment of known binding sites
over negative control primer sets of 5-fold (See Figure 5 below). If the qPCR enrichments are
satisfactory then the remaining 30 µl of ChIP DNA can be used for library generation.
18
16
14
12
10
8
6
4
2
0

18
16
14
12
10
8
6
4
2
0

Poor

lit ChIP
ess t an 5 olenri ment

Cell Line A
Cell Line Bigo signal
strengta gro neg tive Control primer
High

Positive Control primer
lit ChIP

Cell Line A
Cell Line B

o a gro n an moret an 5 ol enri menteg tive Control primer

Positive Control primer

Figure 5: Comparison of qPCR results showing good versus poor enrichment over negative control primers.
Data shows qPCR results analyzed using the ChIP-IT qPCR Analysis Kit with the Human Negative Control Primer as a reference and a gene-specific positive control primer. In the top image the negative control primer set for Cell Line A gives highbackground levels with Binding events detected per 1,000 cells above a value of 2, while Cell Line B has positive control
signal levels below 5 Binding events detected per 1,000 cells. The bottom image shows low background in the negative
control primer set with Binding events detected per 1,000 cells below a value of 2. The fold enrichment of the positive control
primer set exceeds 5-fold. Only the ChIP DNA from the bottom sample is recommended for use in ChIP-Seq.

D. Library Generation
ChIP DNA from the ChIP-IT PBMC Kit has been extensively validated for ChIP-Seq using theIllumina® platform. ChIP DNA can be used to generate single or paired-end libraries using thestandard Illumina® library protocols.
To download an up to date version of the Illumina® library generation protocols, please visit the
Illumina® website at http://support.illumina.com/sequencing/sequencing_kits/chip-seq_dna_sample_prep_kit.ilmn, or search for Catalog No. IP-102-1001.

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Appendix
Section G: qPCR Primer Design and Data Analysis
A. Design of the primers• Design and analyze your potential primer pairs using an in silico PCR program (i.e. Primer3
at http://frodo.wi.mit.edu/ or the UCSC Genome Browser at http://genome.ucsc.edu/cgi-bin/hgPcr).
• Primers that dimerize should be avoided, as they will be bound by SYBR Green, which willcompromise accurate quantitation. You can test your primers for self-complementarity andsecondary structure at http://frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi.
• Ideally, the amplicons should be 75-150 bp in length.
• For use with the ChIP-IT qPCR Analysis Kit, primers should be designed to anneal optimallyat 58°C with a recommended length of 18-22 bp.
• Active Motif offers ChIP Control qPCR primer sets validated to work in our ChIP-IT qPCR
Analysis Kit. To see a list of the available species-specific primers, please visit
www.activemotif.com/chipprimers.
B. Data Analysis
If the data analysis will not be performed using Active Motif’s ChIP-IT qPCR Analysis Kit, two othersimplified methods of analysis are provided below. Both methods listed require the generationof a standard curve, containing known amounts of DNA, for each primer pair being used in theexperiment.
Method 1: Fold enrichment of positive primers relative to negative control primers
1. Produce a standard curve by performing qPCR with your primer set on known DNA
quantities of Input DNA (from Section B Step 17) in triplicate. Run three to five samples
that are 10-fold dilutions, e.g. 0.005 ng, 0.05 ng, 0.5 ng, 5 ng and 50 ng.
2.

Run the ChIP and IgG samples along with the dilution series of the Input DNA standards using both positive control primers (known binding sites) and negative control
primers (regions of the genome not bound by your protein of interest).

3.

Your qPCR instrument will assign values to each qPCR reaction based on the standard
curve. If your machine does not average your triplicate reactions automatically, youwill need to calculate these averages.

4.

Divide the average value from the positive control primer set by the average value ofthe negative control primer set to obtain your fold enrichment.

Method 2: Express data as a percent of input
1. Produce a standard curve by performing qPCR with your primer set on known DNA
quantities of Input DNA (from Section B Step 17) in triplicate. Run three to five samples
that are 10-fold dilutions, e.g. 0.005 ng, 0.05 ng, 0.5 ng, 5 ng and 50 ng.

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2.

Run the ChIP and IgG samples along with the dilution series of the Input DNA standards using both positive control primers (known binding sites) and negative control
primers (regions of the genome not bound by your protein of interest).

3.

Your qPCR instrument will assign values (in ng) to each qPCR reaction based on thestandard curve. If your machine does not average your triplicate reactions automatically, you will need to calculate these averages.

4.

For each qPCR reaction you will have used a percentage of your total ChIP DNA. In
order to calculate the amount in the whole reaction, divide the elution volume of theentire ChIP reaction by the volume used in the qPCR reaction (e.g. if you eluted ChIP
DNA in 200 µl and used 5 µl in the qPCR reaction the formula is 200/5 = 40). Then,
multiply the average qPCR quantity by this number (e.g. qPCR quantity in ng x 40).

5.

To express data as a percent of input, divide the adjusted values from Step 4 above by
the amount of DNA that went into the ChIP reaction and then multiply by 100%. (e.g. if
20 µg was used in the ChIP reaction this is equivalent to 20,000 ng of chromatin. The
calculation would be the adjusted value from Step 4 divided by 20,000 ng and thenmultiplied by 100). Typical percent of input recovered values are 0.05% to 1%.

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21Section H. Troubleshooting Guide
Problem/question

Recommendation

At what points in the
protocol can I stop?

The protocol may be stopped and samples stored at the times and temperatures below:
1. After formaldehyde fixation and centrifugation (intact cell pellet), -80°C.
2. After flash freezing, -80°C.
3. After chromatin shearing, -80°C.
4. After DNA clean up, -20°C.

Poor yield of shearedchromatin.

Insufficient cell numbers were used. Repeat chromatin preparation using a larger numberof cells.
Nuclei not released. Monitor cell lysis under a microscope. Generally, the more cells thatare lysed, the higher the sheared chromatin yield. Vortex cells at highest setting for 30
seconds in the presence of Swelling buffer and Detergent.
Sonication samples were emulsified. Avoid emulsification by turning up the power of thesonicator gradually. If a chromatin preparation becomes emulsified inadvertently, discontinue shearing and centrifuge the sample for 4 minutes at 8,000 rpm in a 4°C microcentrifuge to remove trapped air.
Use fresh formaldehyde when preparing Fixation Solution

Shearing efficiency is notclear from gel analysis.

Material is stuck in the wells, and smears or streaks are seen from the top to bottom of
the lane. The sheared chromatin needs to have the cross-links reversed, protein removed(Proteinase K) and RNA removed (RNase), followed by DNA purification.
High molecular weight products. Decrease the size of the fragments by re-sonicating thesample. If an alternative reverse cross-linking method was used, or the 20 minute incubation at 100°C in NaCl was omitted prior to running the agarose gel for analysis, please
repeat the input chromatin preparation and follow the manual instructions.

Performing ChIP with alarge volume of chromatin.

This is not recommended. It is better to set up several small ChIP reactions (240 μl each)and pool the samples during loading of the DNA purification column, rather than trying
to ChIP a single large sample. Do not perform a single scaled-up reaction, as the capture
efficiency is lower.

ChIP DNA does not turnbright yellow following theaddition of 3 M sodiium
acetateIf the color is light orange or violet, this indicates the pH is too high. Add more 3 M sodium
acetate 5 µl at a time, mixing after addition until the color is bright yellow. This step is
crucial to the success of DNA binding and purification. For a full color image please see themanual for Active Motif’s Chromatin IP DNA Purification Kit Catalog No. 58002 available
online at our website www.activemotif.com.

High background.

Chromatin not sheared enough. Shearing should produce DNA fragments that are smallenough to exclude background from neighboring chromosomal sequences, but still large
enough that there is a good possibility your amplicon remains intact. We recommend
200-1200 bp fragments. If the DNA fragments are too large, the background is increased.
Consider increasing the number of pulses for sonication. Check the fragment size on a gel
to assess your shearing efficiency.
Antibody issue. Too much antibody relative to the amount of chromatin in the ChIP reaction. Excess antibody will result in more non-specific binding, which will be detected asincreased background.

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Problem/question

Recommendation

Poor or no enrichment withtarget antibody.

Too little chromatin. Generally, we recommend using 10 - 30 µg of chromatin per ChIP
reaction. ChIP reactions should not exceed 50 µg per IP reaction. Be sure to quantitate
the concentration of the sheared chromatin sample(s) being ChIP’d to ensure both that
adequate chromatin is used per sample, and that equal mass quantities of chromatin areused in each ChIP.
Antibody is not ChIP validated. The antibody does not efficiently recognize fixed proteins,
either because the epitope is destroyed by fixation or because the epitope is masked byother proteins in a larger complex. To assist in ChIP validating an antibody, it is very usefulto use a positive control antibody such as Histone H3K4me3 (Catalog No. 39915) and anegative IgG from the same species, and primers that have been proven to work in thetype of PCR being used. Active Motif offers species-specific ChIP-IT Control qPCR Kits for
antibody validation (Catalog Nos. 53026, 53027 & 53028).
Low-affinity antibody. Use a different antibody.
Antibody affinity to protein G is weak. Individual monoclonals have variable binding affinities to protein G, which are pH dependent; the optimal pH may vary for each Ig, For thosewith low to medium affinity, capture efficiency by protein G can be dramatically improved
through use of our Bridging Antibody (Catalog No. 53017). This antibody is arabbit anti-mouse pAb that recognizes all subclasses of mouse immunoglobulins. If yourIgG has a weak/medium affinity to protein A or G, the Bridging Antibody will increase
antibody capture by the beads without increasing background.
Problems with PCR. Check the conditions of the PCR master mix used. Confirm the amplified sequence for the positive control primer set is bound by the antibody target. Identify
other binding sites.

No PCR products for the
ChIP’d samples (but the
Input DNA yields thecorrect PCR product)

Increase the amount of chromatin used in the ChIP reaction, the amount of antibody used,or both.

No PCR products with realtime PCR

Confirm the species specificity and efficiency of your primers. You may need to redesign
your primers. Primers that work in end point PCR do not always work in qPCR.

Use a different antibody.

No ethanol in DNA Purification Wash Buffer. Make sure that ethanol has been added to the
DNA Purification Wash Buffer prior to first use.

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23

Technical Services
If you need assistance at any time, please call or send an e-mail to Active Motif Technical Service
at one of the locations listed below.

Active Motif North America
Toll free:Direct:Fax:
E-mail:Active Motif Europe
UK Free Phone:France Free Phone:
Germany Free Phone:Direct:Fax:
E-mail:877.222.9543
760.431.1263
760.431.1351
tech_service@activemotif.com
0800/169 31 47
0800/90 99 79
0800/181 99 10+32 (0)2 653 0001
+32 (0)2 653 0050
eurotech@activemotif.com

Active Motif Japan
Direct: +81 (0)3 5225 3638
Fax: +81 (0)3 5261 8733
E-mail: japantech@activemotif.com
Active Motif China
Direct: (86)-21-20926090
Cell Phone: 18521362870
E-mail: techchina@activemotif.com

Visit Active Motif online at activemotif.com

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