Support | FAQs | SX-8G IP-Star®
Frequently asked questions
- FAQ Sx-8G IP-Star®
- Price of the robot in the US?
- Is it possible to see and/or use the robot?
- What is the procedure following the purchase order?
- How the SX-8G IP-Star installation and training do takes place?
- Computer system: characteristics
- Which are the main advantages of the automated system comparing to the non automated MeDIP and ChIP?
- Which are the automated protocols provided by Diagenode?
- Does Diagenode provide a service for Auto-ChIP, Auto-MeDIP or Auto MBD?
- Which parameters of the protocol can be changed by the user?
- Which are the DNA purification methods that are automated?
- How many samples can be run at the same time?
- Which are the robot dimensions?
- Warranty?
- Maintenance Contract?
- Preventive maintenance to be carried out by the customer
- What is the strength of the magnet?
- What type of material is the deck made of?
- What type of material is the tips made of?
- Are the tips disposable?
- Is the system ventilated?
- How is heating and cooling achieved?
- What is the function of the cooling and heating Pelter blocks?
- Do the Peltier Blocks accept 96 well plates?
- For which application can I use the room temperature 96-well microtiter plates modules?
- What is the basis for DNA-magnetic bead binding during IPure?
- Can the beads be re-used?
- Can the beads be coated with other materials?
- Do we have check points to control the right functioning of the robot?
- Which is the amount of cells that can be used for Auto ChIP?
- Which is the amount DNA that can be used for auto MeDIP?
- Which is the amount DNA that can be used for auto MBD?
- DNA recovery after auto-CHIP or auto-MeDIP? What amount of DNA do you need to start with for DNA amplification? What is the amount of DNA used per array?
- Are the amount of DNA/per reaction enough to proceed with downstream applications
- Is it possible to create an own protocol with own reagents?
- Which beads are included in the auto-ChIP kit?
FAQ Bioruptor® | Tubes, attachments...
- Price of the robot in the US?
- (Price upon request)
The price includes:- Automated System for ChIP and MeDIP
- Computer System
- 1 year Warranty
- Installation
- Software Training
- Validation and Verification for each application purchased (including Diagenode reagents)
- Training on one of the following applications: ChIP, MeDIP or MBD
- Reagents for one of the following:
- 1 x Auto ChIP Kit x16 [AB-Auto01-0016], Sheared chromatin control (sourced separately), primer pairs for ChIP control regions
- 1 x Auto MeDIP Kit x16 [AF-Auto01-0016), Sheared gDNA control (sourced separately), primers pairs for MeDIP control regions
- 100 x 200 μl tube strips (12 tubes/strip) + cap strips [WA-001-0100]
- 500 x tips (filter)
- Is it possible to see and/or use the robot?
- Diagenode will invite leads for a demo “in site”. In some cases demos can be designed in a customer specific way.
In US, the customer could see the SX-8G IP-Star at one of our reference demo sites (West or East Coast).
- What is the procedure following the purchase order?
- Once the purchase order has been placed, the shipment of the robot will take approximately 2 months. During this time the IP-Star specialist contacts the customer to define the training and design possible experiments (ChIP and/or MeDIP).
- Find below an example of such demo and training programme.
GOAL Customer = autonomous for Auto MeDIP/ChIP -
Day 1
9AM Unpacking Calibration Settings PC (incactivate standby modus) Signature bon de reception Sticker
12AM Installation of Protocols
2PM Powerpoint Presentation
- 1st part: Diagenode
- 2nd part: Robot
- Robot
- Software
- Auto Kits and Consumables
- Purification methods
4PM Robot
- How to run MeDIP/ChIP Prot
- How to modify MeDIP/ChIP Prot (Temp. & Incubation time)
Day 2
11AM Robot maintenance instructions
2PM Run AutoMeDIP (Auto Kit, Diagendode Histon Abs)
Training (Ignacio)
Day 3
10AM Recovery Add reagents (Prot K) Of samples (qPCR?) Customers runs own assay
2PM Run Auto-ChIP (Auto Kit, Diagendode Histon Abs)
4PM Discussion
Starting Material needed
- Auto Kits
- Chip grade Histon Abs
- Sheared DNA/Chr.
- Computer system: characteristics
- Processor: AMD ATHLON 5400B (2.8GHz, 512KBX2) [Included in Price]
Operating System: Genuine Windows Vista Business Bonus-Windows XP Professional downgrade
Memory: 1.0GB DDR2 Non-ECC SDRAM, 800MHz, (1DIMM) [Included in Price]
Hard Drive: 80GB SATA, 7200 RPM Hard Drive with Data Burst Cache. [Included in Price]
Monitor: 1024 x 768 monitor (65535)
Slot: optional riser-card cage Slot
- Which are the main advantages of the automated system comparing to the non automated MeDIP and ChIP?
-
- Reproducibility
Between results of different experiments (different operators and labs ). - Consistency
Between different samples in the same experiment. - Time savings
Hands-on-work time reduced to max 1-2h. - Throughput
8IPs/run: protocol is written and validated for MeDIP, ChIP and MBD
16IPs/run: protocol is written and validated for ChIP and MeDIP - Flexibility
Program can be shortened or extended following to your schedule and your needs. It is possible to modify, antibody coating incubation times, IP incubation times and temperatures and time washes. - Standardization
Automation allows easy standardization of a ChIP/MeDIP assay in a lab and between different labs.
- Reproducibility
- Which are the automated protocols provided by Diagenode?
-
- ChIP 8IPs - DIB (100 µl volumes) for 10^3 to 10^7 cells
- ChIP 8IPs – IPure (100 µl volumes) for 10^3 to 10^7 cells
- ChIP 16IPs – DIB (100 µl volumes) for 10^3 to 10^7 cells
- ChIP 16IPs – IPure (100 µl volumes) for 10^3 to 10^7 cells
- ChIP 8IPs - DIB (200 µl volumes) for 10^6 to 5x10^7 cells (TFactors)
- ChIP 8IPs - IPure (200 µl volumes) for 10^6 to 5x10^7 cells (TFactors)
- ChIP 16IPs – DIB (200 µl volumes) for 10^6 to 5x 10^7 cells (TFactors)
- ChIP 16IPs – DIB (200 µl volumes) for 10^6 to 5x 10^7 cells (TFactors)
- MeDIP 8IPs - DIB
- MeDIP 16IPs - IPure
- MethylCap 8IPs One Elution
- MethylCap 8IPs Fraccionated Elution
- IPure 8 samples for ChIP and MeDIP
- IPure 16 samples for ChIP and MeDIP
All ChIP and MeDIP protocols have been validated at Diagenode using chromatin/DNA sheared with the Bioruptor andusing Diagenode antibodies. Each ChIP/MeDIP protocol has been validated using IP times of 5 and 15 hours.
- Does Diagenode provide a service for Auto-ChIP, Auto-MeDIP or Auto MBD?
- Not for the moment
- Which parameters of the protocol can be changed by the user?
- ChIP assay:
- Time for Antibody coating
- Incubation time and temperature for the IP reaction
- Time and stringency of the washes (coming soon)
-
MeDIP assay:
- Incubation time and temperature for the IP reaction
- Time and stringency of the washes (coming soon)
During the training the IP-Star specialist could personalize (if needed) the provided protocols. If later on, the customer wants to make major changes or write a new protocol for a new application, it can also be done at Diagenode. However, in this case customer will have to pay for this service.
- Which are the DNA purification methods that are automated?
- Diagenode offers two different automated protocols for DNA purification after MeDIP and ChIP
- a) DIB purification. Fast and easy method providing good results in qPCR but DNA not pure enough for other downstream analysis.
- b) IPure (using magnetic beads). This method provides DNA of high purity for subsequent amplification, microarray or sequencing.
- How many samples can be run at the same time?
- Diagenode offer protocols for 8 samples/robot run or 16samples/run (for both MeDIP and ChIP) 8 samples run uses 1 heat/cool block (72 samples/ week) 16 samples run uses 2 heat/cool block (144 samples/ week) For ChIP amount of runs per day depends on the IP incubation needed, a parameter which is specific for each antibody
- Which are the robot dimensions?
- Main Body Approx. 1070 (W) x 650 (D) x 779 (H) mm
Weight: 130 kg
- Warranty?
- 1 year
- Maintenance Contract?
- See maintenance contract document.
- Preventive maintenance to be carried out by the customer
- There are three maintenance protocols programmed in the SX-8G IP-Star software and they are well described in the Auto MeDIP, Auto-ChIP, Auto MethylCap and SX8G-IP Star user manuals. The daily maintenance procedure consists in cleaning the worktable and its accessories with 70% ethanol. The workstation can be cleaned with a diluted neutral soap solution whereas the pippeting head channels will be cleaned with distilled water. The weekly maintenance procedure consists in sterilizing the interior of the workstation with the UV lamp, greasing the 0-rings and replacing the O-rings if they are damaged. The monthly maintenance procedure consists in performing an O-ring leakage test fo
- What is the strength of the magnet?
- 300 gauss
- What type of material is the deck made of?
- Aluminium
- What type of material are the tips made of?
- Polypropylene
- Are the tips disposable ?
- Yes, to prevent cross contamination.
- Is the system ventilated?
- Both the upper chamber and the power supply have an active ventilation system
- How is heating and cooling achieved?
- It is achieved through two installed Peltier heating/cooling blocks.
Max temp: 95°
Min temp: 4°
Peltier elements are solid-state devices with no moving parts and they are extremely reliable and do not require any maintenance. They allow cooling below ambient temperature, but unlike other cooling systems (vapour phase refrigeration) they are less expensive and more compact.
One small problem related to Peltier cooling is condensation. That is why Diagenode provides the Peltier devices with a special insulator sponge to eliminate the condensation in the Peltier blocks.
- What is the function of the cooling and heating Pelter blocks?
- Cooling down and heating up is needed during the ChIP and MeDIP protocols. In MEDIP heating is necessary for Elution to release purified DNA from the magnetic beads (in conjunction with a low ionic strength buffer). Cooling is used to reduce evaporation and store samples at 4°C.
For ChIP, reverse crosslinking need temperatures of 65° whereas temperatures for antibody coating and IP are usually 4°C
- Do the Peltier Blocks accept 96 well plates?
- Yes, but not all types. However, Diagenode has only validated the experiment usings 12 tube-strips and 8 tube-strips which allow handling from small to high amount of samples.
- 12 tube-strips: for single IP (less than 8 IPs). Each strip with 12 tubes represents 1 IP reactions. Reagents and material will be distributed in the 12 tube strip according to the indications given in our Auto MeDIP and ChIP manuals.
- 8 tube-strips: if performing complete runs of 8 IPs at the time. Permits a much easier dispending of reagents (same reagent for all the tubes of same strip) and makes the recovery of the samples (all in one strip) much more convenient.
Polypropylene
- For which application can I use the room temperature 96-well microtiter plates modules?
- These modules are specially design for IPure applications. Magnetic DNA purification is done at room temperature.
- What is the basis for DNA-magnetic bead binding during IPure?
- Under chaotropic conditions, DNA has an affinity for silica coated beads. The DNA is released from the beads by addition of a low ionic strength buffer.
- Can the beads be re-used?
- We do not recommend re-use of magnetic beads.
- Can the beads be coated with other materials?
- Yes. For example, streptavidin coated beads may be used to isolate biotin labelled proteins.
- Do we have check points to control the right functioning of the robot?
- Yes we have. For example we have check points when temperatures are set up in the Peltier blocks. The reaction incubation time will not start counting until the temperature of the heat/cool block has reached the temperatures programmed in the automated protocol.
- Which is the amount of cells that can be used for Auto ChIP?
- Chromatin from 10³ to 106 cells can be used for Auto ChIP protocols with 100 µl reaction volumes.
Chromatin from 106 to 5x106 cells can be used for Auto ChIP protocols with 200 µl reaction volumes
NOTE: If the customer is working with primary cells or patient samples like biopsies, the number of cells can be a limitation with the actual protocols.
- Which is the amount DNA that can be used for auto MeDIP?
- 1 µg as starting material (it is the same as for the MagMeDIP kit)
- Which is the amount DNA that can be used for auto MBD?
- 1 µg as starting material
- DNA recovery after auto-CHIP or auto-MeDIP? What amount of DNA do you need to start with for DNA amplification? What is the amount of DNA used per array?
- Auto ChIP (example)
- H3K9me3: Using U2OS cell line
- Starting with 106 cells: DNA recovery ~90 ng/per sample.
- Starting with 3x105 cells: DNA recovery ~20 ng/per sample.
- Starting with 105 cells: DNA recovery ~13 ng/per sample.
- Starting with 104 cells: DNA recovery ~2 ng/per sample.
- Starting with 103 cells: DNA recovery ~0.2 ng/per sample.
- Trans. Factor: Using U2OS cell line
Using Diagenode optimized Antibody/beads/DNA ratio, with a starting material of 1µg usual amounts of pull downed DNA vary between 50-100ng/sample.
- Are the amount of DNA/per reaction enough to proceed with downstream applications ?
- For arrays 250 ng at a minimum are needed and 1-2 ug per array the most likely. For ChIP, there are many factors influencing the recovery of DNA. The final amount recovered depends on cell type, number of starting cells and the antibody. DNA must be pooled or amplified following the next methods: Whole Genome Amplification (WGA), Ligation Mediated-Polymerase Chain Reaction (LM-PCR), or T7 linear Amplification (Method of choice - Diagenode is working actually in a kit for T7 linear amplification).
For MeDIP you should pool up MeDIP samples as well. (~50-100 ng/sample using manual kit) For sequencing 5-10 ng/per ChIP are needed
Auto ChIP experiment with Diagenode histones antibodies and chromatin from 10^5 cells provide in general more than 10 ng of DNA per ChIP reaction. In the case of transcription factors Diagenode recommend in general to use more that 10^6 cells (a good ChIP-grade antibody will be essential to pull down enough target DNA) in order to immunoprecipitate enough DNA avoiding amplification steps
We progress on the validation of the Robot for ChIP-seq (IPure recover higher amount of DNA versus competitor gravity flow columns
- Is it possible to create an own protocol with own reagents?
- Diagenode offer validated protocol in the SX-8G IP-Star automated system with Diagenode reagents and kits. Customer specific protocols can be created and be charged as service.
- Which beads are included in the auto-ChIP kit?
- Both Auto-ChIP kits (the kit 16 and the kit for 100 samples) contain protein A-coated paramagnetic beads. In the case of working with mouse antibodies, protein G-coated paramagnetic beads are available separately.