- Diagenode

AUTO MeDIP KIT MANUAL
Cat. No. C02010011 (AF-Auto01-0016)
C02010012 (AF-Auto01-0100)
Version 7 I 02.14
Technical Assistance & Ordering Information
Diagenode s.a. BELGIUM | EUROPE
Diagenode Inc. USA | NORTH AMERICA
LIEGE SCIENCE PARK
400 Morris Avenue, Suite #101
Rue Bois Saint-Jean, 3
Denville, NJ 07834 - USA
4102 Seraing - Belgium
Tel: +1 862 209-4680
Tel: +32 4 364 20 50
Fax: +1 862 209-4681
Fax: +32 4 364 20 51
techsupport.na@diagenode.com
techsupport@diagenode.com
orders.na@diagenode.com
orders@diagenode.com
For a complete listing of Diagenode’s international distributors, visit:
http://www.diagenode.com/en/company/distributors.php
For the rest of the world, please contact Diagenode s.a.
PAGE 3
Contents
Introduction. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
SX-8G IP-Star Automated System for ChIP, MeDIP &MBD. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
Kit Method Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
Kit Materials. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
Kit Content. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
How to perform Automated MeDIP in the SX-8G IP-Star ® Compact. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
Running a protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
How to perform Automated MeDIP in the SX-8G IP-Star ® . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
Loading and running protocol. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21
Shutting down the SX-8G IP-Star®. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
Quantitative PCR & Data Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
Results. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Troubleshooting Guide. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
Technical Assistance. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
Ordering Information. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Back Cover
www.diagenode.com |
PAGE 4
DIAGENODE AUTO MeDIP KIT USER MANUAL
Introduction
The Diagenode SX-8G IP-Star® Automated System automates immunoprecipitation and
increases reproducibility
Diagenode, the leading provider of complete solutions for epigenetics research, offers a variety of end-to-end systems to
streamline DNA methylation and chromatin immunoprecipitation workflows. Central to this full offering is Diagenode’s
Automated Systems, simple yet robust automated bench-top instruments that standardize different epigenetic
applications (i.e. ChIP, MeDIP or MethylCap). Diagenode designed these automation systems to make ChIP and DNA
methylation studies accessible and reproducible, and ensure consistent data in every experiment.
Diagenode Automated Systems will produce consistent results from any operator regardless of the day, the experimental
run, or the lab. Robust and reproducible results is a major goal of today’s high resolution epigenomic studies.
Diagenode Automated Platforms replace the numerous manual, error-prone steps of complex epigenetic applications
with a reliable, highly consistent and automated process that requires minimal operator intervention. We empower
researchers to simplify the tedious protocols and the complexity of many epigenetic protocols. In addition, Diagenode
Automated Systems minimize sample carryover, data variability, and costly errors. The platforms offer full workflow
support for epigenetics research, utilizing our complete kits and laboratory-validated protocols to rapidly deliver highquality and consistent data.
Auto MeDIP kit
The Diagenode Auto MeDIP kit is designed to perform automated Immunoprecipitate of methylated DNA using the
SX-8G IP-Star.
The Auto MeDIP kit contains the antibody directed against 5-methyl Cytidine as well as meDNA and unDNA internal IP
controls. The IP has been optimized to specifically select and precipitate the methylated DNA: by the use of our antibody,
buffers and protocol. The IP efficiency can indeed be double-checked with the use of our internal controls. Furthermore,
the use of the Automated System will drastically increase the consistency of your MeDIP Assay.
The Auto MeDIP kit allows you to perform DNA methylation analysis of your sample together with optimized internal IP
controls: ALL IN ONE TUBE. The methylated DNA (meDNA) and unmethylated DNA (unDNA) controls allow for direct
CORRELATION between IP’d MATERIAL and METHYLATION STATUS. This methylation analysis is FAST, HIGHLY SPECIFIC
and each IP is QUALITY controlled: essential keys for RELIABLE results.
In the Auto MeDIP kit, the protocol has been improved to allow researchers to work in smaller tubes than traditionally
did so far. The kit ensures the use of low amount of reagents per reaction (not only antibodies, but also buffers) and it
includes fewer buffers in comparison with other kits.
The Kit provides you with a DNA isolation buffer for an extra-fast method to purify your IP’d material (for qPCR analysis).
Alternatively, for other applications, e.g. sequencing, linear amplification or microarray. Magnetic DNA purification
(IPure) protocols can be used as alternative.
Combination of this High Quality Kit and the SX-8G IP-Star Robot will allow you to perform DNA Methyaltion Profiling in
less than 9 hours! Starting with sheared DNA the Automated System will provide you with the purified methylated DNA
of your sample.
The Auto MeDIP kit protocol has been validated using genomic DNA sheared by sonication using the Bioruptor®.
Innovating Epigenetic Solutions
PAGE 5
SX-8G IP-Star® and SX-8G IP-Star® Compact Systems
for automation of epigenetic applications
Diagenode has developed two automated platforms (SX-8G IP-Star® and SX-8G IP-Star® Compact) designed to increase
your lab’s productivity, efficiency and experimental reproducibility. The two automated platforms are capable of processing
up to 16 samples per cycle. The automated systems processes sheared chromatin (or DNA) to deliver purified DNA ready
for qPCR, amplification, microarray and sequencing analysis. Both, the SX-8G IP-Star® and SX-8G IP-star® Compact
have an easy-to-use open software that provides you with flexibility. This allows you to create your personal protocol
according to your specific needs.
Major benefits of Diagenode Automated Platforms
SX-8G IP-Star® Compact SX-8G IP-Star®
> Increased reproducibility
> A consistency “Walk-away research” (less “hands-on-work”)
> Huge time savings
> Easy and flexible programming
> Validated for ChIP, MeDIP & MBD
> Compatible with Diagenode Kits (Auto ChIP kit, Auto Histone ChIP-seq kit, Auto Transcription ChIP kit, Auto
MeDIP kit, Auto MethylCap kit, Auto hMeDIP kit, Auto IPure kit)
> Reduces cross-contamination
www.diagenode.com |
PAGE 6
DIAGENODE AUTO MeDIP KIT USER MANUAL
SX-8G IP-Star® Compact
SX-8G IP-Star®
ChIP-seq, MeDIP-seq, MethylCap-seq,
hMeDIP, IPure, Sample preparation,
Re-ChIP, MagBisulfite, RNA-IP, Library
preparation for NGS platforms.
ChIP-seq, MeDIP-seq, MethylCap-seq,
hMeDIP, IPure, Sample preparation, Re-ChIP,
MagBisulfite, RNA-IP.
User interface
Intuitive touch screen panel
PC Software
User friendly
Software training not required
Software training before use
Dispensing
Automated dispension of assay reagents
Manual dispension of assay reagents
Protocol
optimization
(flexible
parameters)
Antibody coating (temperature, time, mixing
speed)
Immunoprecipitation (temperature, time,
mixing speed)
Washes (temperature, time, mixing speed)
Antibody coating (temperature, time)
Immunoprecipitation (temperature, time)
New protocol
development
Achievable by Diagenode product specialist
Achievable by customer after training
Characteristics
750W x 740 D x 610 H | 100 kg
8 Nozzles X-Y-Z axis | 4 – 95°C
1070W x 650 D x 780 H | 130 kg
8 Nozzles X-Y-Z axis | 4-95°C
Applications
Software
Innovating Epigenetic Solutions
PAGE 7
Improved reproducibility
Our SX-8G IP-Star will increase the immunoprecipitation reproducibility between IPs performed by the same as well as
by different operators (see figure 1 and 2 below). Reagents (Antibodies, buffers,...) and sheared chromatin were identical
for “ManChIP” and “AutoChIP”. The SX-8G IP-Star Automated system removes variation that can be created by manual
handling and allows you to optimize and standardize your assay within a lab. The SX-8G IP-Star is designed to improve
the accuracy and the reproducibility of any immunoprecipitiation experiment.
Man ChIP
SD(IgG)=0,69%
SD(H3K9me3)=23,84%
Man ChIP
SD(IgG)=0,69%
SD(H3K9me3)=23,84%
SD(IgG)=1,4%
SD(H3K9me3)=2,38%
C
% of input
% of input
100,0
80,0
60,0
100,0
40,0
80,0
20,0
60,0
SD(IgG)=0,94%
SD(H3K9me3)=11,36%
SD(IgG)=0,17%
SD(H3K9me3)=1,12%
B
A
ChIP 1
ChIP 1
ChIP 2
SD(IgG)=0,94%
SD(H3K9me3)=11,36%
50,70
ChIP 1
ChIP 2
SD(IgG)=1,4%
98,62
95,26
SD(H3K9me3)=2,38%
ChIP 2
34,63
ChIP 1
ChIP 2
98,62
B
1,96
ChIP 1
D
C
SD(IgG)=0,17%
SD(H3K9me3)=1,12%
57,83
56,25
95,26
A
ChIP 1
SD(IgG)=0,09%
SD(H3K9me3)=0,65%
ChIP 1
ChIP 2
SD(IgG)=0,09%
SD(H3K9me3)=0,65%
44,75
43,83
D
ChIP 2
ChIP 2
57,83
56,25
ChIP 1
0,63 50,70
1,86
1,62
2,06
1,42
1,54
0,63
1,86
1,62
2,06
1,42
1,54
ChIP 2
1,42 44,75
43,83
34,63
40,0
Figure 1: Manual ChIP. Four different
operators have each performed two ChIP
experiments using H3K9me3 antibody
on the genomic region SAT2 (positive
locus). 10,000 Hela cells have been used
per IP. Reagents and sheared chromatin
were identical per assay. The standard
deviations between the ChIPs performed
by the same operator and between the
four different operators are displayed.
20,0
1,96
1,42
Auto ChIP
SD(IgG)=0,28%
SD(H3K9me3)=1,6%
Auto ChIP
SD(IgG)=0,28%
SD(H3K9me3)=1,6%
100,0
90,0
% of input
% of input
80,0
ChIP 2
ChIP 1
70,0
100,0
ChIP 3
54,71
56,25
60,0
90,0
ChIP 4
57,83
54,34
50,0
80,0
40,0
70,0
ChIP 2
ChIP 1
ChIP 3
54,71
56,25
30,0
60,0
ChIP 4
57,83
54,34
20,0
50,0
10,0
40,0
30,0
1,00
1,26
IgG
H3K9me3
IgG
1,45
H3K9me3
IgG
Figure 2: Automated ChIP. Four ChIP
experiments using H3K9me3 antibody
on the genomic region SAT2 (positive
locus) have been performed by the SX8G IP-Star. 10,000 Hela cells have been
used per IP. Reagents and sheared
chromatin were identical per assay. The
standard deviations between the four
ChIPs performed by the SX-8G IP-Star
are displayed.
0,81
H3K9me3
IgG
H3K9me3
20,0
10,0
1,00
1,26
IgG
H3K9me3
IgG
1,45
H3K9me3
IgG
0,81
H3K9me3
IgG
H3K9me3
www.diagenode.com |
PAGE 8
DIAGENODE AUTO MeDIP KIT USER MANUAL
Kit Method Overview
Chromatin/DNA Shearing
Chromatin/DNA Preparation
(Bioruptor® Sonication)
Increased Reproducibility
Chromatin Shearing
Optimization kit (Low SDS,
Medium SDS and High SDS)
STEP
1
Automated & High -Throughput
No “Foaming”
ST
E
No Risk of Contamination
P
2
Next Gen Sequencing
Bioruptor® Pico
Auto MethylCap Kit
nds-on time
10 min
15
STEP 4
DNA Purification
IPure kit
(magnetic purification)
DNA Isolation Buffer
S
mi
n
P
TE
6
EP
5m
Ha
ST
3
Auto hMeDIP Kit
in
Auto MeDIP Kit
m
DNA Methylation
EP
Auto Transcription ChIP kit
ST
Auto True MicroChIP Kit
Auto Histone ChIP-Seq kit
20
Chromatin study
in
Magnetic IP
Size Selection
with AMPure® XP beads
5
Library Preparation
Illumina® TruSeq™ ChIP
NEBNext® ChIP-seq
MicroPlex Library Preparation kit
(50 pg, multiplex, manual)
qPCR
Figure 3. Diagenode provides a full suite of automated solutions for ChIP experiments.
For Step 1, we offer products to isolate nuclei and chromatin. Step 2 describes reproducible sample shearing with the Bioruptor® product
line. In Step 3 and Step 4, the Diagenode IP-Star Compact provides error-free, walk-away automation for all your immunoprecipitation
and antibody capture needs.
Innovating Epigenetic Solutions
PAGE 9
Kit Materials
Kit Content
Two Auto MeDIP Kit formats are available and the kit content is sufficient to perform either 16 or 100 MeDIP assays by
using the SX-8G IP-Star Automated System. The kit content is described in Table 1. Upon receipt, store the components
at the temperatures indicated in Table.
Table 1. Kit content
Description
Quantity (x16)
Quantity (x100)
Storage
Magbeads
250 µl
1.3 ml
4°C (do not freeze)
Water
3 ml
20 ml
4°C
MagBuffer A (5x)
3 ml
20 ml
4°C
MagBuffer B
150 µl
1000 μl
4°C
MagBuffer C
60 µl
400 μl
- 20°C
Antibody anti-5meC
10 µl
50 μl
- 20°C (-80°C)
meDNA Positive control
40 µl
40 μl
- 20°C
unDNA Negative control
40 µl
40 μl
- 20°C
MagWash buffer-1
10 ml
60 ml
4°C
MagWash buffer-2
6 ml
40 ml
4°C
DNA Isolation Buffer (DIB)
6 ml
40 ml
4°C
Proteinase K
60 µl
400 μl
-20°C
Primer pair #1 (meDNA control)
50 µl
50 μl
-20°C
Primer pair #2 (unDNA control)
50 µl
50 μl
-20°C
Reference
Quantity
Storage
200 µl tube strips (12 tubes/strip) + cap strips
WA-001-0080
80
RT
200 µl tube strips (8 tubes/strip)
+ cap strips for SX-8G IP-Star® Compact
WA-002-0120
120
RT
Tips (bulk)
WC-001-1000
1000
RT
Tips (box)
WC-002-0960
10x96
RT
Comments
Reference
Quantity
For easy and fast
DNA extraction
mc-magme-003
60 rxns
Table 2. Components available separately
Description
Table 3. Modules available separately
Description
XL GenDNA Extraction Module
www.diagenode.com |
PAGE 10
DIAGENODE AUTO MeDIP KIT USER MANUAL
Table 3. Kits and Modules available separately
Description
Reference
Quantity
Chromatin shearing optimization kit - Low SDS
C01020010 (AA-001-0100)
1 kit
Chromatin shearing optimization kit - Medium SDS
C01020011 (AA-002-0100)
1 kit
Chromatin shearing optimization kit - High SDS
C01020012 (AA-003-0100)
1 kit
AL-100-0100
100 rxns
AL-Auto01-0100
100 rxns
IPure
Auto IPure
Table 4. Plastics and consumables available separately
Description
200 μl tube strips (12 tubes/strip) + cap strips
200 μl tube strips (8 tubes/strip) + cap strips for SX-8G IP-Star Compact
®
Reference
Quantity
WA-001-0080
80 pc
WA-002-0120
120 pc
96 well microplates
WA-003-0010
10 pc
Tips (box)
WC-002-0960
960 pc
WC-001-1000
1000 pc
2 ml microtube for SX-8G IP-Star Compact
WA-008-0100
100 pc
Large reagent container for SX-8G IP-Star® Compact
WA-007-0020
20 pc
Medium reagent container for SX-8G IP-Star Compact
WA-006-0010
10 pc
Tips (bulk)
®
®
Innovating Epigenetic Solutions
PAGE 11
How to perform Automated MeDIP in the SX-8G IP-Star®
Compact
A. Prepare Reagents
1. Preparation of MagBuffer A (1x) (for 1 IP) in 1.5 ml tube.
MagBuffer (1x)
200 µl
MagBuffer A (5x)
40 µl
Water
160 µl
B. Prepare Antibody and IP Mixes
2. Preparation of Antibody Dilution (1:2) (max. 6 IP) in 1.5 ml tube.
Antibody (1:2)
2 µl
Antibody
1 µl
Water
1 µl
3. Preparation of Antibody Mix in 1.5 ml tube.
Antibody Mix
One IP
For 2 IPs
For 4 IPs
For 6 IPs
For 8 IPs
Antibody 1:2
0.30 µl
0.75 µl
1.50 µl
2.00
3.00 µl
MagBuffer A (5x)
0.60 µl
1.50 µl
3.00 µl
4.00
6.00 µl
Water
2.10 µl
5.25 µl
10.50 µl
14.00
21.00 µl
MagBuffer C
2.00 µl
5.00 µl
10.00 µl
13.00
20.00 µl
FINAL VOLUME
5.00 µl
12.50 µl
25.00 µl
33.00
50.00 µl
4. Preparation of Incubation Mix (1 IP + 1 Input) in 1.5 ml tube.
Incubation Mix
90 µl
H2O
45 µl
MagBuffer A (5x)
24 µl
MagBuffer B
6 µl
meDNA positive control
1.5 µl
unDNA negative control
1.5 µl
Sheared DNA (0.1 µg/µl)
12 µl
a. Incubate at 95°C for 3 minutes
b. Quickly chill on ice (it is best to use ice-water)
c. Perform a short spin at 4°C.
Note: The incubation mix is prepared in excess. 75 µl will be needed for the IP.
d. Take 7.5 µl incubation mix and store it in a new tube. This is the input.
Before dispensing, mix the content in the tube by pippeting up and down.
5. Preparation of Immunoprecipitation Mix (for 1 IP) in 1.5 ml tube.
Immunoprecipitation Mix
100 µl
MagBuffer A (1x)
20 µl
Incubation Mix
75 µl
Antibody Mix
5 µl
www.diagenode.com |
PAGE 12
DIAGENODE AUTO MeDIP KIT USER MANUAL
Running a protocol
Diagenode Splash Screen – A0
After the software start-up screen disappears, the Diagenode splash
screen is displayed for several seconds, and then disappears.
Start Screen – Top menu
After the Digenode splash screen disappears, the start screen is
displayed. This is the first active window; it allows the user to enter into
three different parts of the software.
USER ACTIONS:
Buttons:
• Protocols
• Maintenance (for technical services)
• Information (for Diagenode contact details)
Protocols screen
All available protocols are displayed on this screen.
Innovating Epigenetic Solutions
PAGE 13
Screen – [Categories Name] Protocol List
After the user presses the “[Categories Name]” button, the “[Categories
Name]” appears. When selected the protocol on the protocol list, the
“Run” button shall turn executable.
Buttons:
• T
he user presses the “Back” button. The user returns to the
“Protocols” screen.
• T
he user presses the “Shutdown” button. The screen shall be
changed to “Power Off”.
• T
he user presses the “Run” button. The screen shall be changed
to “Sample number”.
• Page up the list box.
• Page down the list box
Screen – Sample number
After the user presses the “Run” button, the “Sample number” appears.
Buttons:
• T
he user presses the “Sample number” Text box. The screen will
be changed to keyboard.
• T
he user presses the “Back” button. The user returns to the
“Protocol List” screen.
• T
he user presses the “Next” button. The screen shall be
changed to “Configuration” or “Layout information”.
Keyboard
www.diagenode.com |
PAGE 14
DIAGENODE AUTO MeDIP KIT USER MANUAL
Screen – Configuration
After the user presses the next button from the “Sample number” screen,
the “Configuration” screen appears.
Buttons:
• T
he user presses the “Back” button. The user returns to the
“Protocol List” screen.
• T
he user presses the “Next” button. The screen shall be
changed to “Layout information”.
• T
he user presses the “Save Parameter” button. The screen will
be changed to “Save Parameter - Confirmation”.
- OK – Current parameters shown in the Display View will
be stored to the [Protocol].ptd. And, returns the user to the
display of the “Configuration” screen.
- No – Returns the user to the display of the “Configuration”
screen.
• T
he user presses the Text box. The screen will be changed to
Keyboard or Speed list menu.
Keyboard
Speed list menu
Innovating Epigenetic Solutions
PAGE 15
Screen – Layout Information
After the user presses the “next” button from “Sample number” screen or
“Configuration” screen, the “Layout Information” screen appears.
Buttons:
Layout information
• T
he user presses the “Back” button. The user returns to the
previous screen.
• T
he user presses the “Next” button. The screen changes to “Set
confirmation”.
• W
hen the user presses a block, that block is magnifies on the
work surface layout background. The magnified view provides a
better display of the correct method setup for that block on the
work surface.
• B
ased on the selected protocol, the user follows the indications
provided in the screens to set up correctly the different reagents
and samples based on the selected ChIP protocol.
Block-Tip
Block-Regent Tip Rack
Block-PCR Tube
www.diagenode.com |
PAGE 16
DIAGENODE AUTO MeDIP KIT USER MANUAL
Select a Protocol name
Input value in the
“Sample Number”
Input value in the
“Configuration”
Current Temperature Value
Screen – Set confirmation
After the user presses the “next” button in the “Layout information” screen, the “Set confirmation” screen appears.
At this point, user is expected to be ready to press RUN.
Buttons:
• The user presses the “Back” button. The user returns to the layout information screen.
• T
he user presses the “Run” button. This is the expected action when user gets to this display after reviewing
blocks. Runs the protocol.
Protocol name
Progress Bar
Remaining time
Current Temperature Value
Screen – Running
After the user presses the “Run” button in the “Set confirmation” screen, the “Running” screen appears.
Buttons:
• The user presses the “Stop” button. The screen changes to “Stop Dialog”.
Status screen is preferred as a progress bar that moves across the screen as the step progresses
Innovating Epigenetic Solutions
PAGE 17
Screen – Running status
This screen gives informations about the current
running step of the protocol.
The user can check through this screen the
passed and remaining time of the experiment.
A. MeDIP - DIB
B. MeDIP - IPure
Screen – Elution
Screen – Elution
INPUT is defined as
INPUT= 7.5µl Incubation Mix + 92.5 µl
DIB buffer
INPUT is defined as
INPUT= 7.5 µl Incubation Mix + 92.5 µl Elution
Buffer (IPure kit)
IMPORTANT: Please note that the enriched methylated
DNA in DIB buffer is single strand DNA that can be
directly analyzed by qPCR. For downstream applications
such as sequencing or arrays, the enriched methyated
DNA needs to be purified by phenol/chroloform
extraction and converted to double stranded DNA.
IMPORTANT: Please note that the enriched methylated DNA is
single stranded DNA that needs to be purified before analysis.
DNA can be purified following IPure automated protocols and
Diagenode's Auto IPure kit (see Auto IPure kit user manual)
Alternatevely, the enriched methylated DNA could be purified
by phenol/chroloform extraction or using spin columns. For
downstream applications such as sequencing or arrays, the
enriched methyated DNA needs to be converted to double
stranded DNA.
Screen – Finish/End
When the protocol is complete, a window appears telling user the run
is over. The screen behind this window should be the Startup screen.
When OK is pressed, then the Startup screen appears and the user can
immediately begin to remove their sample and prepare the next run.
At this point, user is expected to be ready to press RUN.
Buttons:
• T
he user presses the “OK” button. Then screen shall be changed
to “[Categories Name] Protocol List”.
www.diagenode.com |
PAGE 18
DIAGENODE AUTO MeDIP KIT USER MANUAL
Screen – Caution !
When the protocol finishes the user can return
to the protocol list (screen A.) or warm the
peltier block (screen B.) to eliminate possible
condensation in the block.
A.
Innovating Epigenetic Solutions
B.
PAGE 19
How to perform Automated MeDIP in the SX-8G IP-Star®
A) Prepare Reagents
1. Preparation of MagBuffer A (1x) (for 1 IP) in 1.5 ml tube.
MagBuffer (1x)
200 µl
MagBuffer A (5x)
40 µl
Water
160 µl
B) Prepare Antibody and IP Mixes
2. Preparation of Antibody Dilution (1:2) (max. 6 IP) in 1.5 ml tube.
Antibody (1:2)
2 µl
Antibody
1 µl
Water
1 µl
3. Preparation of Antibody Mix in 1.5 ml tube.
Antibody Mix
One IP
For 2 IPs
For 4 IPs
For 6 IPs
For 8 IPs
Antibody 1:2
0.30 µl
0.75 µl
1.50 µl
2.00
3.00 µl
MagBuffer A (5x)
0.60 µl
1.50 µl
3.00 µl
4.00
6.00 µl
Water
2.10 µl
5.25 µl
10.50 µl
14.00
21.00 µl
MagBuffer C
2.00 µl
5.00 µl
10.00 µl
13.00
20.00 µl
FINAL VOLUME
5.00 µl
12.50 µl
25.00 µl
33.00
50.00 µl
4. Preparation of Incubation Mix (1 IP + 1 Input) in 1.5 ml tube.
Incubation Mix
90 µl
H2O
45 µl
MagBuffer A (5x)
24 µl
MagBuffer B
6 µl
meDNA positive control
1.5 µl
unDNA negative control
1.5 µl
Sheared DNA (0.1 µg/µl)
12 µl
a. Incubate at 95°C for 3 minutes
b. Quickly chill on ice (it is best to use ice-water)
c. Perform a short spin at 4°C.
Note: The incubation mix is prepared in excess. 75 µl will be needed for the IP.
d. Take 7.5 µl incubation mix and store it in a new tube. This is the input.
Before dispensing, mix the content in the tube by pippeting up and down.
www.diagenode.com |
PAGE 20
DIAGENODE AUTO MeDIP KIT USER MANUAL
5. Preparation of Immunoprecipitation Mix (for 1 IP) in 1.5 ml tube.
Immunoprecipitation Mix
100 µl
MagBuffer A (1x)
20 µl
Incubation Mix
75 µl
Antibody Mix
5 µl
C) Dispense prepared reagents into the corresponding tubes (see picture below)
Note: Reagents dispension is different depending on the DNA purification method selected.
Loading reagents: make sure that all reagents are in the bottom of the tubes (especially magnetic beads) before
starting the protocol.
DIB
Tube #
IPURE
Description
Volume
Description
1
DNA isolation buffer
92.5 µl
-
Volume
-
2
Empty
-
-
3
Magnetic beads
10 µl
-
4
MagBuffer A (1x)
50 µl
Elution buffer (IPure kit)
50 µl
5
MagBuffer A (1x)
50 µl
MagBuffer A (1x) + beads
50 µl + 10 µl
6
-
7
Immunoprecitation Mix
8
9
-
MagBuffer A (1x)
50 µl
100 µl
Immunoprecitation Mix
100 µl
MagWash buffer-1
100 µl
MagWash buffer-1
100 µl
MagWash buffer-1
100 µl
MagWash buffer-1
100 µl
10
MagWash buffer-1
100 µl
MagWash buffer-1
100 µl
11
MagWash buffer-2
100 µl
MagWash buffer-2
100 µl
12
DNA isolation buffer
100 µl
Elution buffer (IPure kit)
50 µl
1. For IPure method, Input sample will be purified following the IPure kit instructions.
2. For MeDIP-IPure experiments See intructions in the Auto IPure manual to prepare the Elution Buffer (Buffer A+ B)
DIB
DNA isolation buffer (Input)
Bead washes
Washes
MeDIP
1
2
3
4
IPure
5
6
7
8
9
10
11
DNA isolation buffer (IP)
12
Second elution and final sample position
Bead washes
Washes
MeDIP
1
2
3
4
5
6
7
8
9
10
11
First elution
12
IMPORTANT: At the end of the MeDIP-IPure reaction, 100 μl of IP sample are collected from well 4
Innovating Epigenetic Solutions
PAGE 21
MeDIP protocols provided for the SX-8G IP-Star
Volumes
8 IP's
100 µl
16 IP's
100 µl
DIB
IPure
Loading and running protocol
Be sure that the computer connected to the robot never switches to the standby modus. (standby modus has to
be inactivated). Standby of the computer will lead to the abort of the protocol.
1. Switch on the SX-8G IP Star. The power switch is on the right side of the instrument.
2. Switch on the computer.
3. Start SX-8G V52 software through SX-8G V52 the following icon
4. Place the prepared tube strip on the right cooling / heating block of the workstation
11
0
5. Close the workstation door and lock it using the following icon 6. Press the following icon Select the protocol of interest. Press start.
www.diagenode.com |
PAGE 22
DIAGENODE AUTO MeDIP KIT USER MANUAL
IMPORTANT NOTE:
1. If the MeDIP protocols do not appear on the screen, Open the SX-8V52 directory and open Easy start ini file. Write
the directory location of the protocols.
2. The Easy start ini file should contain the following information:
[EASYSTARTSCREEN]
HoldFilePath=C:\Documents and Settings\Desktop\New software protocols\ MeDIP
In red is indicated the the directory location of the MeDIP protocols
3. Start now SX-8G V52 software through SX-8G V52 exe.file
4. Press button for Easy Protocol Start screen and load the protocol of interest
Before starting the protocol a start confirmation window will appear. Press OK and the protocol will run.
Alternatively, temperature and incubation time for the IP reaction can be modified in an existing protocol by selecting
the modify button. The modified protocol can be also saved as new protocol.
Innovating Epigenetic Solutions
PAGE 23
7. The program will run through the following steps: magnetic
bead washes, IP and IP washes.
During protocol the next window will be displayed indicating the
current protocol step.
8. a) MeDIP-DIB
After the IP washes the following window will be appear.
Follow the next instructions:
1. Add 7.5 µl of Incubation Mix (Input) to well 1
2. Add 1 µl proteinase K to wells 1 and 12
3. Close the tube strip with the corresponding caps
4. Press OK
7.5 µl input + 1 µl Proteinase K
IP DNA isolation
+ 1 µl Proteinase K
1
2
3
4
5
6
7
8
9
10
11
12
IMPORTANT: Please note that the enriched methylated in DIB buffer is single strand DNA that can be directly
analyzed by qPCR.
For downstream applications such as sequencing or arrays, the enriched methyated DNA needs to be purified by
phenol/chroloform extraction and converted to double stranded DNA.
www.diagenode.com |
PAGE 24
DIAGENODE AUTO MeDIP KIT USER MANUAL
8. b) MeDIP-IPure
Follow the next instructions:
1. Collect samples from well 4 and keep them at 4 degrees
2. F
ollow instructions from the Auto IPure kit manual to proceed with the DNA purification of the samples and the
input
IMPORTANT: Please note that the enriched methylated in DIB buffer is single strand DNA that can be directly
analyzed by qPCR.
For downstream applications such as sequencing or arrays, the enriched methyated DNA needs to be purified by
phenol/chroloform extraction and converted to double stranded DNA.
9. The following window will appear:
Close the workstation door and press OK.
The program will move forward to the next steps of the MeDIP protocol.
10. The SX-8G IP-Star software indicates the end of the protocol.
Collect your immunoprecipitated and isolated DNA
11. Discard magnetic beads by using the DiaMag02 (cat# kch-816-001) or by centrifugation.
12. This is your DNA ready for qPCR.
Shutting down the SX-8G IP-Star
1. Click on File and press End to close the software correctly.
2. Switch off the computer and its monitor.
3. Switch off the SX-8G IP-Star Automated System (power switch on the right side).
Note: Ensure that the door is closed!
Innovating Epigenetic Solutions
PAGE 25
Quantitative PCR & Data Analysis
The Methylated DNA IP module includes four validated primer pairs specific to four types of DNA:
1) methylated DNA control (primer pair #1)
2) unmethylated DNA control (primer pair #2).
3) methylated human DNA region (testis-specific H2B, TSH2B)
4) unmethylated human DNA region (GAPDH promoter)
Note: Primer pairs for mouse and rat are available! Please visit www.diagenode.com
1.Prepare your qPCR mix using SYBR Green PCR master mix and start out qPCR.
qPCR mix (total volume of 25 µl/reaction):
- 1
.00 µl of provided primer pair (stock: 10 µM each: reverse and forward)
- 1
2.50 µl of master mix (e.g.: iQ SYBR Green supermix)
- 5
.00 µl of isolated DNA or diluted purified DNA sample (see above for DNA dilutions)
- 6
.50 µl of water
Table 1. qPCR cycles:
Temperature
Time
Cycles
95°C
7 minutes
x1
95°C
15 seconds
60°C
60 seconds
95°C
1 minute
x1
65°C and increment of 0.5°C per
cycle
1 minute
x60
PCR
Amplification
Melting curve
x40
2.When the PCR is done, analyse the results. Some major advices are given below.
• Data interpretation
he efficiency of methyl DNA immunoprecipitation of particular genomic locus can be calculated from qPCR data
T
and reported as a recovery of starting material: % (meDNA-IP/ Total input).
% (meDNA-IP/ Total input)= 2^[(Ct(10%input) - 3.32) - Ct(meDNA-IP)]x 100%
ere 2 is the AE (amplification efficiency), Ct (meDNA-IP) and Ct (10%input) are threshold values obtained from
H
exponential phase of qPCR for the methyl DNA sample and input sample respectively; the compensatory factor
(3.32) is used to take into account the dilution 1:10 of the input. The recovery is the % (meDNA-IP/ Total input).
• Background determination
he final goal of IP is to calculate the enrichment in the same IP sample of: 1/ the specific DNA fragments
T
(corresponding to the hydroxymethylated DNA) in comparison with 2/ non-methylated DNA (i.e. negative unDNA
control).
• Relative occupancy can be calculated as a ratio of specific signal over background.
Occupancy= % input (specific loci) / % input (background loci)
Relative occupancy is then used as a measure of the hydroxymethylation of a specific locus; it provides clues about
specificity of the IP. (background loci) corresponds to the signal obtained with one of the unmethylated DNA kit
control.
www.diagenode.com |
PAGE 26
DIAGENODE AUTO MeDIP KIT USER MANUAL
Results
Figure 1: Automated MeDIP (9h)
Automated Methyl DNA IP (9h)
(IP reaction
during
Automated
Methyl
DNA 5h)
IP (9h)
(IP reaction during 5h)
Automated Methyl DNA IP (19h)
(IP reaction during 15h)
Automated Methyl DNA IP (19h)
(IP reaction during 15h)
IP reaction was performed with the
anti-5meC antibody. Methylated and
unmethylated DNA were used as
internal controls. Unmethylated DNA
region of GADPH and a methylated
DNA region of AlphaX1 were used
to test DNA sample-IP efficiency.
DNA has been isolated by using DNA
isolation buffer.
Figure 2: Automated MeDIP (19h)
IP reaction was performed with the
anti-5meC antibody. Methylated and
unmethylated DNA were used as
internal controls. Unmethylated DNA
region of GADPH and a methylated
DNA region of AlphaX1 were used
to test DNA sample-IP efficiency.
DNA has been isolated by using DNA
isolation buffer.
Troubleshooting Guide
Error Cause
Remedy
SX-8G IP-Star cannot be switched on
SX-8G IP-Star is not receiving power. Check that the power cord is connected to the
workstation and to the wall power outlet.
Computer cannot be switched on
Computer is not receiving power. Check that the power cord is connected to the
computer and to the wall power outlet.
SX-8G IP-Star shows no movement when a
protocol is started
SX-8G IP-Star is not switched on. Check that the SX-8G IP-Star is switched on.
SX-8G IP-Star shows abnormal movement
when a protocol is started
The pipettor head may have lost its home position. In the Software, select “Manual
Operation/Home”. After confirming that the pipettor head moves to the home
position, run the protocol again.
Aspirated liquid drips from the disposable
tips
Dripping is acceptable when ethanol is being handled. For other liquids: air is leaking
from the syringe pumps. Grease or replace the O-rings. If the problem persists,
contact DIAGENODE Technical Services.
Innovating Epigenetic Solutions
Technical Assistance
At DIAGENODE we pride ourselves on the quality and availability of our technical support. Our Technical Services
Departments are staffed by experienced scientists with extensive practical and theoretical expertise in molecular biology
and the use of DIAGENODE products. If you have any questions, or experience any difficulties regarding the SX-8G IPStar or DIAGENODE products in general, do not hesitate to contact us.
DIAGENODE customers are a major source of information regarding advanced or specialized uses of our products. This
information is helpful to other scientists as well as to the researchers at DIAGENODE. We therefore encourage you to
contact us if you have any suggestions about product performance or new applications and techniques.
For technical assistance and more information call the DIAGENODE Technical Service Department or contact your local
distributor.
www.diagenode.com |
Ordering information
Description
Cat. No. (NEW)
Cat. No. (OLD)
Format
SX-8G IP-Star® Compact
B03000002
UH-002-0001
1 unit
Auto True MicroChIP kit
C01010140
/
16 rxns
Auto True MicroChIP & MicroPlex Library Prep Package
C01010141
/
16 ChIP rxns & 12 library
prep rxns
MicroPlex Library Preparation kit x12
C05010010
AB-004-0012
12 rxns
Auto Histone ChIP-seq kit protein A x16
C01010020
AB-Auto02-A016
16 rxns
Auto Histone ChIP-seq kit protein A x100
C01010022
AB-Auto02-A100
100 rxns
Auto Histone ChIP-seq kit prowwtein G x16
C01010021
AB-Auto02-G016
16 rxns
Auto Histone ChIP-seq kit protein G x100
C01010023
AB-Auto02-G100
100 rxns
Auto Transcription ChIP kit protein A x16
C01010030
AB-Auto03-A016
16 rxns
Auto Transcription ChIP kit protein A x100
C01010032
AB-Auto03-A100
100 rxns
Auto Transcription ChIP kit protein G x16
C01010031
AB-Auto03-G016
16 rxns
Auto Transcription ChIP kit protein G x100
C01010033
AB-Auto03-G100
100 rxns
Auto ChIP kit protein A x100
C01010011
AB-Auto01-A100
100 rxns
Auto ChIP kit protein G x100
C01010013
AB-Auto01-G100
100 rxns
Auto MeDIP kit x16
C02010011
AF-Auto01-0016
16 rxns
Auto MeDIP kit x100
C02010012
AF-Auto01-0100
100 rxns
Auto hMeDIP kit x16
C02010033
AF-Auto02-0016
16 rxns
Auto MethylCap x48
C02020011
AF-Auto01-0048
48 rxns
Auto IPure kit
C03010010
AL-Auto01-0100
100 rxns
Visit us at one of Diagenode’s demo sites or discover our Automated Systems by performing some assays with the help of our R&D and Technical Department.
diagenode headquarters
www.diagenode.com
Diagenode s.a. BELGIUM | EUROPE
LIEGE SCIENCE PARK
Rue Bois Saint-Jean, 3
4102 Seraing - Belgium
Tel: +32 4 364 20 50 | Fax: +32 4 364 20 51
orders@diagenode.com
info@diagenode.com
Diagenode Inc. USA | NORTH AMERICA
400 Morris Avenue, Suite #101
Denville, NJ 07834 - USA
Tel: +1 862 209-4680 | Fax: +1 862 209-4681
orders.na@diagenode.com
info.na@diagenode.com
For a complete listing of Diagenode’s international
distributors visit:
www.diagenode.com/en/company/distributors.php
For rest of the world, please contact Diagenode s.a.
© 2013 Diagenode, Inc. All rights reserved. The content of this document cannot be reproduced without prior permission of the authors. Bioruptor and IP-Star are registered trademarks of Diagenode.
MA-AMeDIP-V7_02_14
Download PDF