FAQ

General Axela Questions

dotLab Questions

dotLab mX System

dotLab Sensors

Sample preparation and analysis

Software

Ziplex Questions

Sample Preparation Kit

TipChips

Ziplex Automated Workstation

Gene Expression Services


GENERAL Axela questions

Q: How do I contact Axela Service and Support?

A: You can either call us at 416-798-1625 or toll free at 1-866-84-AXELA (29352) or email us at email.

Q: How to I order Axela products and consumables?

A: Visit our Catalogue page on this website to create a shopping list and then visit one of our distributors to place the order.

Q: Does Axela offer a preventative maintenance schedule  on its systems?

Yes. Call Axela Service and Support at 416-798-1625 or toll free at 1-866-84-AXELA (29352) and speak to a Service Representative for details.

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dotLab Questions


dotLab mX System

Q: What is diffractive optics technology and how does it work?

A: As a beam of light passes through an optical grating, it splits and diffracts generating a predictable pattern of beams. The intensity of these beams correlates to the thickness of the optical grating. Therefore, changes in grating thickness can be determined by measuring the intensity of the diffracted beams. Diffractive optics technology utilizes this principle to monitor molecules as they bind or dissociate from an optical grating.

Q: How does the dotLab mX System detect molecular interactions in real time?

A: The dotLab mX System uses diffractive optics to monitor molecular interactions in real time. These interactions occur in disposable, plastic biosensors each containing a contiguous array of optical gratings made up of affinity reagents. As samples are delivered to the sensor by the dotLab mX System, the gratings are illuminated with a laser and the intensity of one of the diffraction beams is monitored in real time. As molecules bind to the grating, the intensity of the diffraction beam increases and conversely, as molecules dissociate the intensity decreases.

Q: What is the sensitivity of the dotLab mX System?

A: Detection sensitivity on the dotLab mX System is mainly dependent on two factors: 1) the size of the molecule; 2) the occupancy or percentage of the binding sites on the sensor that is occupied. Therefore, detection sensitivity is higher for large molecular weight molecules (eg: antibodies). Low molecular weight molecules can be directly detected without amplification if present in sufficient molar quantities to occupy a sufficient number of binding sites. Detection sensitivity can be significantly increased by using amplification strategies that either directly or indirectly increases the apparent size of the binding molecule (eg: antibodies, nanoparticles/beads, enzyme-mediated precipitation). By utilizing these amplification strategies, a dynamic range of over 7-Logs can be achieved.

Q: Is the dotLab mX only used for protein interaction analysis?

A: The dotLab mX is capable of analyzing any molecular interactions as long as one of the analytes can be immobilized to the sensor surface. These include protein-nucleic acid, nucleic acid-nucleic acid, protein-carbohydrate etc.

Q: What are the dimensions of the dotLab mX System and how much does it weigh?

A: The dimensions of the dotLab mX System are as follows: 435 mm (17.11”) H x 579 mm (22.81”) W x 693 mm (27.27”) D. The instrument weighs 47.6 kg (105 lbs).

Q: Does the dotLab mX System have any special power requirements?

A: The dotLab mX can be plugged into any conventional 100-240 V AC, 50/60 Hz power outlet.

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dotLab Sensors

Q: What kind of sensors are currently available?

A: We currently offer sensors with three different immobilization chemistries: 1) avidin; 2) covalent; 3) panelPlus. The avidin sensor is used to immobilize biotinylated capture molecules. The covalent sensors have an amine reactive surface that covalently binds molecules containing primary amine groups. panelPlus sensors contain unique oligonucleotides on each of the spots within a sensor. Different capture molecules can be addressed to different spots on a sensor by conjugating them to the respective complementary oligonucleotide strand. panelPlus sensors can therefore be used to perform multiplexed assays.

Q: How do I store and handle a sensor?

A: All sensors should be stored between 4-8⁰C and handled carefully to avoid damage and contamination of the diffraction grating.

Q: What is the self life of a sensor?

A: No more than one year.

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Sample preparation and analysis

Q: What kind of samples can be analysed on the dotLab mX System?

A: A wide variety of crude, complex biological samples can be analysed on the dotLab mX System including serum/plasma, whole blood, stool filtrate, cell/tissue/plant extracts and urine.

Q: How are samples delivered to the sensors?

A: The dotLab mX includes an integrated fluidic handling system which follows user defined steps to deliver samples from 96-well plates or up to three different bulk reagent bottles to the sensors. Samples can be applied to the sensors in either one-directional continuous flow, statically or by back and forth mixing.

Q: How long do typical assays take on the dotLab?

A: Assay time can vary significantly depending on the number of steps involved and user defined incubation times, but are generally much faster than ELISA or Western blot. For example, a typical sandwich immunoassay would take about 30 minutes to perform.

Q: What kind of buffers can I use?

A: The dotLab mX System is compatible with all buffers that are used in routine immunoassays or nucleic acid hybridizations.

Q: What volume of sample is required?

A: Typically, 5-30 µL of sample is required for mix incubation in a sensor. With serum/plasma or cell/tissue lysates, samples are often diluted 10-fold in sample diluent so approximately six microlitres of original sample is needed.

Q: Can I recover the molecules captured in the sensors for subsequent analysis by other methods?

A: The sensors come in a lidless format allowing you to recover its contents with the appropriate elution buffer. This material can then be used by other methods such as mass spectrometry for further characterization.

Q: How do I analyse the data generated on the dotLab mX?

A: The amplitude of binding curves or the initial rate of binding are used to quantitate binding events. In capture assays, these values are normalized to the amplitude of the capture molecule binding step to account for slight variations in sensor binding capacity. Data analysis can be performed using the quantitation feature of the dotLab Software.

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Software

Q: What kind of computer hardware/software is required to operate the instrument?

A: The dotLab mX instrument comes with an integrated MacIntosh Mini computer, monitor and wireless keyboard. The computer runs on the Mac OS operating system and comes pre-loaded with the dotLab Software which is used for instrument control and data analysis.

Q: Are dotLab data files compatible with PC-based computers?

A: dotLab method, schedule and quantitation files can be exported in Adobe pdf format and viewed on PC-based computers. Data files are exported in .daf format and can be viewed on PC-based computers using the Daf Viewer software, available free of charge from Axela.

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Ziplex Questions


Sample Preparation Kit

Q: What sample preparation kit does Axela recommend?

A: Axela recommends using the Ambion TotalPrep™ RNA Amplification Kit (Cat# AMIL1791) which is based on the in vitro transcription protocol developed by James Eberwine (Van Gelder et al. 1990).

Q: What kind of samples can I use with the Ziplex System?

A: Blood and tissue samples are compatible for use with the Ziplex System.

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TipChips

Q: What is the shelf-life of TipChips and what are the storage requirements?

A: 6 months when stored between 2 – 8oC.

Q: Do TipChips require special handling?

A: TipChips should be handled with care taken to avoid any damage to the wafer.

Q: How many times can I use a TipChip?

A: The TipChip is designed to be a single-use item.

Q: What is the difference between Xpress Chips and Autograph Chips?

A: Xpress Chips are pre-configured TipChips targeting gene signatures for various diseases and conditions. Autograph Chips are custom-designed TipChips for a customer specific application. Contact your Distributor or Axela Services and Support for more details on ordering Autograph Chips.

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Ziplex Automated Workstation

Q: Can the system be run overnight?

A: Yes. The Ziplex System is designed to run unattended and will enter a standby mode once the run is complete

Q: Is there a warm-up period for the Ziplex Automated Workstation when I first turn it on?

A: No. The system is ready for use as soon as you turn it on

Q: Does the Ziplex Automated Workstation require a system flush or lengthy shut-down procedure?

A: No. If the Workstation will be inactive for more than a week, we recommend you simply turn the instrument and monitor power off. There is no lengthy system shut-down procedure required.

Q: Is there a risk of contamination from run to run?

A: It is extremely important to discard both the TipChips and the uniplates after each run. This prevents run to run contamination and ensures that you will get accurate results with the Ziplex System.

Q: How do I order more 96-well Uniplates®?

A: Axela recommends using the Whatman 96-well Uniplate. These can be ordered directly from Whatman with Cat# 7701-1651.

Q: What are the dimensions of the Ziplex Workstation and how much does it weigh?

A: The dimensions are as follows: 36” x 27” x 36” (HxDxL). It weighs 115kg or 250Ibs.

Q: Does the Ziplex Automated Workstation require special power requirements?

A: The Ziplex requires a voltage input of 90-135 V AC (50/60 Hz).

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Gene Expression Services

Q: Will my data and samples be kept confidential?

A: Yes. Axela maintains confidentiality on all customer services projects.

Q: How do I format my gene list before sending it to Axela?

A: A Microsoft Excel worksheet file format is recommended. Please list each sequence, probe, or gene symbol ID entry on a different line of the same column. Please provide NCBI RefSeq RNA gene IDs when possible. Other information that permits the reliable identification of accession numbers in public databases is also acceptable.

Q: What protocol do you follow to design probes for my target genes?

A: We identify a list of NCBI RefSeq RNA database sequence IDs that correspond to your genes. A validated probe design software package is then used to identify unique sequence regions in each gene sequence and to design probes within these regions. Our software then ranks all potential probes according to how well they conform to Axela's Ziplex System requirements.

Q: How do I send my samples to Axela for analysis?

A: Samples should be packed in a well insulated styrofoam container with at least 6kg of dry ice and shipped overnight to Axela. Axela will provide you with a Sample Submission Form, instructions on how to pack / ship samples, a sample commercial invoice and FedEx Expanded Service Waybill and account number. Please contact your Sales Manager or Customer Service for more information.

Q: How much of each sample do I need to send?

A: Generally we request that each customer send 1.2μg of each sample: approximately 200ng for sample QC and two 500ng aliquots for separate amplification reactions. We have, however, successfully amplified smaller amounts of sample in the past (as little as 500ng of total RNA). Talk to your Sales Manager if you have sample quantities significantly smaller than our recommended amount.

Q: What controls do you use?

A: Axela TipChips have several types of control probes as follows:

  • Every TipChip has control probes for assessing hybridization selectivity.
  • Probes targeting the 5' and 3' regions of commonly used housekeeping genes are used to assess amplified sample quality.
  • Negative control probes targeting non-human sequences are present to measure hybridization background signal levels and specificity.

Additionally, during sample amplification several aliquots of control RNA are amplified in parallel with the customer samples. Each control sample yield and quality is measured and compared to expected results to ensure consistency of the amplification reagents and technical performance.

Q: What do I receive at the end of the project?

A: At the end of the project Axela will provide you with a report which will include a summary of the sample QC and amplification results as well as Axela's expert analysis of the project results.

Q: What happens to remaining samples that are not used for my project?

A: Samples are discarded after a period of two years from date of receipt unless other arrangements are made.

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