Support | FAQs | SX-8G IP-Star®

Frequently asked questions SX-8G IP-Star®

System Specifications

Auto ChIP Assays

Automated DNA Methylation Assays

Automated IPure

Automated Library Preparation Assays


System Specifications


Auto ChIP Assays


Automated DNA Methylation Assays


Automated IPure


Automated Library Preparation Assays


FAQ SX-8G IP-Star® | System Specifications

What does the SX8G IP-Star® price include?
The price of the IP-Star® system includes:

- Automated System for Epigenetic applications
- 1 year Warranty
- Installation and training by Diagenode Application Scientist
- Validation and Verification for each application purchased (including Diagenode reagents)
- Training on one of the following applications: ChIP and/or MeDIP
- Reagents and consumable needed for the training

What is the procedure following the purchase order?
Once a customer purchase an SX-8G IP-Star® unit has been placed, Diagenode will contact the customer to set up the dates for the installation and training
Which are the robot dimensions?
Main Body Approx. 800 (W) x 700 (D) x 675 (H) mm Weight: 97 kg
Throughput of the system
Up to 16 samples per run
What applications are automated in the IP-Star®?
ChIP, MeDIP, MethylCap,hMeDIP, Bisulfite Conversion, RNAIP, Illumina True-seq genomic Library prep, ReCHIP and DNA purification.
Do I get updates on the IP-Star® software and future automated protocols?
Yes, if Diagenode upgrades the software, the updated software will be sent to the customer with instructions for the installation. If Diagenode develops new automated protocols/applications, the new protocols will be sent to the existing customers with instructions for the installation.
What are the working volumes in the IP-Star®?
The IP-Star® automated system handle volumes from 5ul to 200ul.
Can I use my own reagents?
Yes, the IP-Star® ais a flexible platform that allows using own reagents for some of the automated applications.
What is the shelf life for the Diagenode reagent kits?
We recommend using them within 6 months the kit is opened upon receipt. For long term storage, kits can be kept up to 2 years when respecting the storage conditions.
`
Is it possible to create an own protocol with own reagents?
Diagenode offers validated protocols in the SX-8G IP-Star® automated system with Diagenode reagents and kits. Any applications based on the use of magnetic beads can be potentially automated in the IP-Star® Compact. Diagenode offers services to customize specific applications
Is the IP-Star® guaranteed?
1 year included in the price. The warranty includes one visit per year for general maintenance of the system. Warranties can be extended for periods of 1,2 or 3 years
What is the regular maintenance required by the IP-Star®?
The daily maintenance procedure consists in cleaning the worktable and its accessories. The workstation and accessories can be cleaned using diluted neutral soap solution or 50% ethanol solutions.

The weekly maintenance procedure consists in greasing the 0-rings in the nozzles. The nozzles can be cleaned with distilled water prior to be greased.

The monthly maintenance procedure consists in performing an O-ring leakage test.

In addition, if the IP-Star® is under warranty, Diagenode will perform general maintenance once per year.
What to do if I observe liquid leakage from Tip-end or big difference in liquid level among lanes?
Two possibilities:

- O-rings are not greased enough or O-rings are deteriorated.
- Disposables are not set properly

What is the strength of the magnet?
3000 gauss
What type of material are the tips made of?
Low binding Polypropylene
Are the tips disposable?
Yes, to prevent cross contamination.
Can the beads be re-used?
We do not recommend re-use of magnetic beads.
It is possible to use magnetic beads coated with other materials?
Yes. For example, streptavidin coated beads may be used to isolate biotin labeled proteins.
Can I use any type of magnetic beads?
We recommend using magnetic beads provided by Diagenode in order to assure optimal performance and sample handling of the automated system
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 (vapor 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 Peltier blocks?
The use of Peltier block assures constant temperature during the runs. I.e. cooling and heating is needed during applications such as ChIP (antibody coating and IP are performed at 4°C whereas reverse crosslinking need temperatures of 65°) or MeDIP. The use of Peltier blocks allows reducing evaporation and samples storing at 4°C after run finishes.
How many Peltier blocks does the IP-Star® system have?
2 Peltier Blocks
Does the Peltier Blocks accept 96 well plates?
Yes, but not all types. However, Diagenode provides 12 tube-strips and 8 tube-strips which allow handling from small to high amount of samples. The strip tubes are made of polypropylene
For which application can I use the room temperature 96-well microtiter plates modules?
These modules are specially designed for magnetic bead based DNA purification technologies such as IPure (DNA purification protocol based on the use of magnetic beads). Magnetic DNA purification is done at room temperature. This module is also used for automated Illumina DNA Library preparation applications
How should we clean up the system?
Clean the system by wiping it with paper towel for laboratory use wetted with 70% ethanol. Avoid the area where electronic parts are located and where grease is coated. The nozzle area may have a black silicone ring coated with silicone grease, depending on the systems. Please note that the removal of the silicone grease may lead to inadequate fitting of the pipetting tip and leakage (liquid leakage).

FAQ SX-8G IP-Star® | Auto ChIP assays

What are the ChIP steps that are automated in the IP-Star®?
The ChIP steps that automated in the IP-Star® are beads equilibration in immunoprecipitation buffer, Antibody coating, IP step, IP post washes, DNA elution and DNA purification steps. In order to perform ChIP experiments in the IP-Star®, the user needs to prepare and shear in advance the chromatin for the experiments.
What type of ChIP protocols can I run in the IP-Star®?
The IP-Star® system allows you running ChIP Direct protocols or ChIP Indirect protocols. ChIP direct protocols refer to those in which an Antibody coating on the beads is performed prior to the inmunoprecipitation step. ChIP Indirect protocols refer to those in which the inmunoprecipitation step is performed prior to the incubation of the magnetic beads with the immunocomplex.
Can I modify parameters in the ChIP protocols through the software?
Auto ChIP protocols in the IP-Star® Compact are very flexible and adapted for testing important variables that might affect the success of your ChIP experiments. Defining the different conditions and parameters for your Auto ChIP experiments is easy since the IP-Star® Compact is provided with a friendly graphic user interface. When running Auto ChIP Direct protocol you can easily define the incubation times and temperatures for the antibody coating, inmunoprecipitation and washing steps. When running Auto ChIP Indirect protocols you will be able to define the incubation times for the inmunoprecipitation, beads incubation and washing steps. Through the user interface it you can define the mixing speed during all incubation steps. At the same time the flexibility of the IP-Star® compact allows testing different type of reagents and compare and run side by side different chromatin and antibodies amounts as well as different types of chromatin and antibodies .
Which is the minimum amount of chromatin I can use for ChIP experiment the IP-Star® Compact?
Diagenode has been able to validate some antibodies in Auto ChIP experiments when using as low as 200 cells per experiment.
Why is important the chromatin fixation step for the outcome of my Auto ChIP experiments?
Poor crosslinking causes DNA loss, elevated background, and/or reduced antigen availability in chromatin. Empirically determine optimal crosslinking time for maximal specificity and efficiency of Auto ChIP. The optimal duration of cross-linking varies between cell type and protein of interest. Short crosslinking time (5-10 minutes) may improve shearing efficiency. Crosslinking duration should not exceed 30 minutes or shearing will be inefficient.
Why fixation time is important?
Crosslinking may be too weak or too strong without proper fixation time. Optimize fixation step e.g.: incubate for 8 minutes at room temperature with high-quality, fresh 1% formaldehyde final concentration (weight/volume).
What is the optimal formaldehyde concentration for the chromatin fixation?
Lower formaldehyde concentrations (1%weight/volume) may improve shearing efficiency. For some proteins, however, especially those that do not directly bind DNA, this might reduce crosslinking efficiency and thus the yield of precipitated chromatin. Empirically determine the formaldehyde concentration as some antigen epitopes may be more sensitive to formaldehyde.
Should I use fresh chromatin or can I use frozen chromatin for my Auto ChIP experiments?
Samples can be frozen at several steps of the protocol. Snap freeze and thaw on ice (e.g. fixed cell pellets and sheared chromatin). Pellets of formaldehyde fixed cells can be stored at -80˚C for at least a year. Sheared chromatin can be stored at -80ºC for months, depending on the protein of interest. Avoid multiple freeze/thawing.
How important is SDS concentration in my ChIP experiments?
High % SDS favors better sonication but inhibits immunoselection . Optimal SDS concentration for shearing is from 0.1% to 1%). Optimal SDS concentration for IP steps is antibody- dependent and in general it should not be higher than 0.15 to 0.20% (e.g. if the shearing buffer contains 0.75% SDS, the sheared chromatin is diluted 3.5 to 4.0 fold in the ChIP buffer). For ChIP-seq experiements, Diagenode recommends using Shearing Optimization kit with low SDS concentration (0.1%)
How can I prepare the chromatin for my automated ChIP experiments?
Diagenode recommends using the Bioruptor shearing system in combination with Diagenode Chromatin Shearing Optimization kits to deliver high quality sheared chromatin to be used in the IP-Star® Compact. Please note that sheared chromatin should be supplied in 100 or 200ul volumes in order to perform Auto ChIP experiments
What type of Auto ChIP kits are offered by Diagenode?
Diagenode offers three types of Auto ChIP kits (Auto ChIP kit, Auto Histone ChIP-seq kit and Auto Transcription ChIP kit) that differ in the buffers composition. For detailed information about the kits, please contact Diagenode technical support at customersupport.na@diagenode.com or customersupport@diaghenode.com
Do the Auto ChIP kits provide Protease Inhibitors?
Yes but the cocktail provided do not include phosphatase inhibitors.
Why is my antibody not working in Auto ChIP experiments?
  1. Antibody-antigen recognition can be significantly affected by the cross-linking step resulting in loss of epitope accessibility and/or recognition.
  2. Use only the antibody of high quality, ChIP-grade.
  3. The best ratio: antibody per amount of chromatin has to be used in ChIP assay.
  4. Do not forget to dilute the sheared chromatin (if it contains ionic detergents such as SDS) before immunoselection incubation step. In general, SDS concentrations below 0.2% would allow antibodies to work in immunoprecipitations reactions
I get a lot of background in my Auto ChIP experiments?
The software of the IP-Star® allows you to increase the time of your washing steps in order to reduce background when necessary.At the same time, Diagenode offers three types of Auto ChIP kits that differ in buffers compositions allowing you to work with washing buffers with low or high stringency. Pre-clearing the chromatin with BSA, preblocking the beads is also possible when doing Auto ChIP experiments in the IP-Star®
Which is the DNA recovery after using Diagenode Auto ChIP kits?
The results of our studies show that for the histone antibodies we can expect between 10-20ng of DNA from 10^6 cells. However the yield will vary depending on starting number of cells, antibody quality, the target - transcription factor or histone modification, and the quality of the starting sample material. Please also note that the amount of DNA that is immunoprecipitated does not necessarily indicate the percentage of specific to non-specific DNA.
Which type of beads is included in the Auto ChIP kits?
Diagenode Auto-ChIP kits (the kit 16 and the kit for 100 samples) are provided with Protein A-coated paramagnetic beads or Protein G-coated paramagnetic beads. Magnetic beads can be separately purchased when researcher performs the automated experiments using own reagents.
Should I use Protein A or protein G coated paramagnetic beads in my Auto ChIP experiment?
The use of protein A or protein G coated paramagnetic beads depends on the isotype and source of your antibody. Please contact the technical support at customersupport@diagenode.com or at customersupport.na@diagenode.com for further information
Can I use paramagnetic beads from other companies?
Beads from other suppliers might have different sizes, binding capacities and magnetic properties so they might not behave optimally with the automated protocols provided by Diagenode
What is the binding capacity of Diagenode coated magnetic beads?
10ul of Diagenode Protein A or Protein G coated paramagnetic beads can bind up to 2.5ug of Antibody.
What type of antibodies can I use for my ChIP experiments?
Diagenode recommends using ChIP-grade antibodies to perform the automated ChIP experiments in the IP-Star®.
How do I select the right antibody for my ChIP experiments?
Use ChIP-grade antibodies or several antibodies directed against different epitopes of the same protein. Verify that the antibodies work directly in IP on fresh cell extracts. When testing new antibodies, include known ChIP-grade antibodies as a positive control. Be aware of the possible cross-reactivity of antibodies. Verify by Western blot analysis the antibody specificity. Antigen affinity purification can be used to increase titer and specificity of polyclonal antibodies
What is the amount of antibody per ChIP to use?
It should be determined empirically for each target and antibody. For abundant proteins, like histones, use 1 to 2 µg of affinity purified or monoclonal antibody per IP. For other targets, use up to 10 µg per ChIP. To ensure efficient IP it is important to have an optimal ratio between the amount of chromatin, amount of antibody and amount of beads. More quantity of antibody (or less chromatin) can be required in case of low affinity to antigen or high abundance of target protein (e.g. histones). Insufficient amount of antibody can result in low efficiency of ChIP whereas large excess of antibody might lead to lower specificity
Can I use automated protocols to purify the sample after ChIP?
Diagenode offers two different automated protocols for DNA purification compatible with MeDIP, hMeDIP, MethylCap, Re-ChIP and ChIP applications

a) DIB purification. Elution in DIB buffer with proteinase K treatment. Two incubation steps. First at 55°C and second at 95°C to inactivate proteinase K before qPCR. Fast and easy method providing good results in qPCR but DNA not pure enough for other downstream analysis such as sequencing or arrays.
b) IPure. Reverse crosslinking is performing at 65°C for 4 hours in the presence of salt. After that, DNA is purified on 96-well plates with IPure kit using magnetic beads. This method provides DNA of high purity for subsequent amplification, microarray or sequencing.


FAQ SX-8G IP-Star® | Automated DNA methylation assays

Which is the starting DNA amount required for Auto MeDIP, hMeDIP and MethylCap protocol?
Use 1 µg DNA/reaction as starting material for each application. When using different DNA amounts, optimization of reaction parameter might be needed.
What is the optimal range of DNA fragment size for Auto MeDIP and Auto MethylCap experiments?
The average range after sonication is between 200-500bp
How can I shear my DNA for performing automated experiments to pull down methylated DNA?
Diagenode recommends using the Bioruptor Standard or Bioruptor Plus to sheared your DNA when using automated protocols in the IP-Star® Compact to pull down methylated DNA. Diagenode technical support can provide you with protocols to fragment your DNA at size ranges that goes from 150bp to 2000 bp.
What happens after DNA shearing? DNA will be denatured and degraded as well?
DNA shearing leads to DNA fragmentation, but do not lead to DNA degradation. Optimal fragment average size for MeDIP and MethylCap experiments is about 500bp. Sheared DNA has to be denaturated in order to facilitate antibody binding to 5-methylcytidin.
Can you recommend the sonication conditions to obtain 300-500bp fragments?
It is advised to optimize the shearing conditions "in house" with your own sample. Generally we recommend using 300 µl of your DNA sample resuspended at 0.1µg/µl (30µg DNA) in 1,5 ml tube with the settings as below:

Bioruptor power: Low, Cycles: 15 s ON and 15s OFF, Total sonication time: 10-15min

Can Auto MeDIP kit be used with DNA obtained from paraffin-embedded samples?
Diagenode has not tested its MeDIP kits for immunoprecipitation of DNA from paraffin-embedded samples. It should be possible to perform MeDIP but note, that the quality of DNA from paraffin-embedded samples is not optimal for MeDIP. The fixation introduces DNA modifications (addition of mono-methyl group, formation of bridges between adjacent bases, generation of apurinic and apyrimidinic sites and strand breaks). DNA quality varies from sample-to sample. However, our customers have successfully used the antibody anty-5methyl cytidine (the same as used in our MeDIP kits) in immunohistochemistry assay on fixed sections.
Is the Auto MeDIP kit suitable for comparing DNA methylation of bacterial DNA?
Our MeDIP kit can be used for the DNA methylation studies in different organisms. In the kit we use the antibody raised against 5-methyl-cytosine. In bacteria the methylation happens on cytosine and adenosine residue; so our kit can be used only for cytosine methylation studies.
What kind of experimental controls are included in the Auto MeDIP kit?
There are two controls included in the kit: positive and negative (methylated DNA and unmethylated DNA) spike DNA controls and two primers pairs to analyze the corresponding fragments. These internal controls will help you to assure the good function of the antibody during the IP step.
What size fragments would be expected from the amplification of your positive and negative controls?
Amplified region with positive control primer is 81bp; negative control amplifies a PCR product of 92bp.
Do the methylated and unmethylated DNA controls interfere with the experimental input DNA that will be immunoprecipitated?
No. It does not interfere with any kind of DNA except the DNA from Arabidopsis, because the Methylated and Unmethylated DNA controls are coming from Arabidopsis thaliana. After the shearing, the corresponding DNA has been enzymatically modified with Sassy methylate in vitro in order to produce the Methylated DNA.
How long I can store antibody from the Auto MeDIP kit at -20°C? How long can I store MAB-5MECYT-100 from my separate order at -20°C?
5-methyl-cytidine antibody (separate or from the kit) is quite fragile, so the best way is to store at -80°C. Aliquot the antibody and avoid multiple freeze-throw. It can be stored at -20°C for 1 month. Do not store at 4°C, it degrades rapidly.
How long can I store the aliquot antibody at -80°C?
The antibody is stable at least for 1 year at -80°C. Aliquot the antibody and avoid multiple freeze-throw
What is the typical yield of the immunopreciptated DNA I Auto MeDIP experiments?
The recovery after MeDIP can vary for different cell type but an average recovery is between 20-50ng per IP (when using 1ug DNA as starting material). Note that recovered DNA is in single stranded conformation. Measuring the DNA concentration choose corresponding option at Nanodrop. Consequently, fluorophore-based DNA measurement (as Picogreen) is not suitable as it specific for dsDNA.
After immunoprecipitation, do I get single-stranded or double-stranded DNA?
Methylated DNA is single-stranded
Can I use automated protocols to purify the sample after MeDIP?
Diagenode offers two different automated protocols for DNA purification compatible with MeDIP, hMeDIP, Re-ChIP and ChIP applications

• a) DIB purification. Elution in DIB buffer with proteinase K treatment. Two incubation steps. First at 55°C and second at 95°C to inactivate proteinase K before qPCR. Fast and easy method providing good results in qPCR but DNA not pure enough for other downstream analysis.

• b) IPure. Reverse crosslinking is performing at 65°C for 4 hours in a buffer with salt. After, DNA is purifying on 96-well plate with IPure kit using magnetic beads. This method provides DNA of high purity for subsequent amplification, microarray or sequencing.

What steps can I take to get best possible enrichment in Auto MeDIP experiments?
- Use the correct concentration of antibody as recommended in the manual.
- Double check the amount of DNA and antibody.
- Use the recommended ratio of antibody to DNA – the ratio is critical.
- Always use fresh dilutions of antibody (within the same day).
- Avoid excessive freeze-thaw of the antibody – you may aliquot the antibody upon receipt, freeze the aliquots, and prepare fresh dilutions before each use.
Has been the Auto MeDIP kit validated for MeDIP-seq applications?
Yes, please refer to the IP-Star® publications section in the website
Recommendations for performing Auto MeDIP experiment for sequencing analysis?
  1. Diagenode recommends sonicating the DNA so that the peak of material is quite short (150-250bp); using the Diagenode' Bioruptor® Standard or Bioruptor®Plus. Contact Diagenode technical support for getting additional information about the shearing protocol or try the following conditions
  2. Total time: around 40-50 min, Cycles: 30s ON, 30s OFF, Power settings: LOW Tubes: 0.65 ml Diagenode tubes, Shearing Volume in the tubes: 100 µl. A Cooling system is recommended in order to get less sample-to sample variation.
  3. Diagenode recommends following the Auto MeDIP-seq protocol described in the following publications:
Butcher LM, Beck S, AutoMeDIP-seq: A high-throughput, whole genome, DNA methylation assay, Methods,2010 ,52,223-231, http://www.ncbi.nlm.nih.gov/pubmed/20385236
Taiwo O, Wilson GA, Morris T, Seisenberger S, Reik W, Pearce D, Beck S, Butcher LM, Methylome analysis using MeDIP-seq with low DNA concentrations., Nat Protoc,2012-03-08,7,617-36, http://www.pubmed.org/22402632
What kind of experimental controls are included in the Auto hMeDIP kit?
The Auto hMeDIP kit contains hmeDNA, meDNA and unDNA internal spike DNA controls. The kit also provides primers to analyze the spike DNA controls. In addition to that, mouse primer pairs for a Sfn1 hydroxylmethylated genomic region are included the kit.
Which antibodies are provided in the Auto hMEDIP kit?
The hMEDIP kit can be purchased with three different antibodies: rat 5-hmC monoclonal antibody, mouse 5-hmC monoclonal antibody or rabbit 5-hmC polyclonal antibody.
What type of MDB protein is included in the Auto MethylCap kit?
The MethylCap protein consists of the methyl binding domain (MBD) of human MeCP2, as a C-terminal fusion with Glutathione-S-transferase (GST) containing an N-terminal His6-tag.
How should I store the MethylCap protein?
The MethylCap protein is very sensitive to temperature changes. Store the protein at -80°C and Avoid multiple freeze-thaw cycles.
What automated protocols are included in the IP-Star®?
There are two types of MethylCap automated protocols in the IP-Star®. The protocols differ in the way the elution of the methylated DNA is done. You can run automated protocols to pull down and elute the methylated DNA in one elution step (MethylCap One Elution) or you can pull down and eluted the methylated DNA based on the density of methylated CpG islands (Methyl Cap Fractionated Elution).
How should be the DNA preparation prior to run Automated MethylCap in the IP-Star®?
DNA should be sheared in 300-500 bp fragments.
What is the shearing protocol recommended for preparing DNA for MethylCap experiments?
Using the Bioruptor-Standard or Birouptor Plus

  1. In a 1.5 ml tube, dissolve the DNA samples in GenDNA TE to reach 0.1 μg/μl.
  2. Use a final volume of 300 μl of DNA samples in 1.5 ml tubes.
  3. Shear the DNA using the Bioruptor® (http://www.diagenode.com/).
Power: High,Cycles: [15 seconds "ON" & 15 seconds "OFF"],Total time: 10 minutes
What do I get after the Auto MethylCap pull down assay?
Methylated double stranded DNA.
Is the Auto MethylCap kit compatible with all downstream applications?
Yes, but eluted DNA should be de-salted.
How should I prepare the DNA in order to perform Auto MagBisulfite experiments in the IP-Star®?
The DNA should be pure (A260/280 ratio between 1.7 and 1.9) and be diluted in 22.5μl water or TE buffer Pure DNA should be used. Optimal quantities of DNA to use are from 100ng - 1μg. The lowest DNA quantity used with then kit should be 1 ng.
What is the throughput of MagBisulfite experiments in the IP-Star®?
The MagBisulfite Automated protocols can process up to 8 samples in parallel.
I get incomplete conversion?
• Check the purity of DNA sample. Proteins and RNA contaminations affect the conversion rate. • DNA is not completely denaturated: make sure that freshly prepared 3M NaOH is used. • Ensure that no more than 1 μg of DNA is used per reaction. The excess of DNA in conversion reaction reduces the efficiency.
No PCR products in control reaction
• Make sure that DNA polymerase used is not inhibited by uracil in the converted sequence.Non-proofreading Hot Start Taq-polymerase is recommended. • Bisulfite conversion reagent prepared/stored incorrectly. Ensure that only freshly prepared. Conversion Reagent is used. • Amount of starting DNA is outside of recommended range. Incomplete desulphonation: be sure that desulfonation reaction is carried out at 42°C.

FAQ SX-8G IP-Star® | Automated IPure

What is the main principle of the Auto IPure protocol?
Magnetic beads acquire positive charge to bind the negatively charged phosphate backbone of DNA. DNA-bead complex is separated using a magnet, washed twice and eluted in water (Buffer C)
Is the Auto IPure compatible with all applications?
Auto IPure has been validated to be used to purified sheared DNA after Auto ChIP, Auto MeDIP and Auto MethylCap experiments with One Elution step.
What type of Auto IPure protocols are provided in the IP-Star®?
The IP-Star® offers two types of protocols IPure and IPure-seq protocol that only differ in the final elution volume of the sample. IPure protocols elute in 50 ul in buffer C . IPure-seq protocols elute samples in 20 ul Buffer C and are compatible with volumes requested by the Illumina and NEB Library prep kits.
What are the main factors affecting the efficiency of the purification?
Two factors are important in order to have a good efficiency of DNA purification:

  1. Concentration of NaCl in the Elution buffer used in the ChIP, MeDIP or MethylCap should be above 200mM. Diagenode recommends using the Elution Buffer (Buffer A and Buffer B) provided in the IPure kit to be used as Elution buffer in your ChIP, MeDIP and MethylCap protocols.
  2. Adding a carrier is necessary to increase the efficiency of the binding step when working with samples with low DNA concentration (i.e ChIP,MeDIP or MethylCap)
  3. DNA Fragment size: Auto IPure protocols have been validated using 100-500bp DNA fragments. Shorter fragments than 100 bp won't bind to the beads in Auto IPure protocols.
  4. DNA starting amount: Auto IPure protocols have been optimized to work with starting DNAs amounts from 5 ng to 1 ug of DNA. Below 3 ng efficiency of Auto IPure decreases considerably
Can I use Auto IPure protocols to purified genomic DNA?
Diagenode has only validated Auto IPure protocols when using sheared DNA from ChIP, MeDIP or MethylCap samples. Genomic DNA can be purified using Auto IPure protocols when using DNA from 5 ng to 1 ug DNA

FAQ SX-8G IP-Star® | Automated library preparation assays

Which library preparation steps are automated in the IP-Star® Compact?
The IP-Star® automates the library prep steps corresponding to : End repair, A-tailing ,ligation and corresponding purifications steps using magnetic bead based DNA purifications technology. Size selection is not currently automated in the IP-Star®
How many libraries can I prepare in the IP-Star®?
The IP-Star® automated library prep protocols can process 8 samples at time.
What types of libraries can I prepare using the IP-Star® automated system?
There are currently validated automated protocols for genomic library preparation using Illumina True-seq kits.
What is the starting DNA amounts required for DNA library prep?
Diagenode IP-Star® Automated systems is capable to prepare libraries using from 50 ng to 1 ug of genomic DNA
Can I index libraries using the IP-Star® Compact?
Yes. Each individually indexed adapter will placed in a separate tube for ligation to the individual library fragments.