Product FAQ

What is “celpaircheckstatus,” and what does it do?

Answer

Celpaircheckstatus checks if the results from the AT channel are consistent with the results from the GC channel and represent the results of the respective channel. This metric will be “out of bounds,” for example, when the AT and GC channels were mispaired between samples or due to sample contamination. We recommend troubleshooting as described in the OncoScan™ Console User Manual.

Answer Id: E13863

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Product FAQ

What does “low diploid flag” mean?

Answer

The algorithm identifies normal diploid markers in the cancer samples. This is particularly important in highly aberrant samples. The normal diploid markers are used to calibrate the signals so that a log2 ratio of 0 (e.g., copy number 2) is achieved. In about 2% of samples, the algorithm cannot identify a sufficient number of “normal diploid” markers, and no normal diploid calibration occurs. This event triggers “low diploid flag = YES.” In this case, the user needs to carefully examine the log2 ratios and verify that re-centering is necessary.

Answer Id: E13864

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Product FAQ

Can I create my own reference set?

Answer

We have not enabled the capability for customers to create their own reference sets. (This process requires careful sample selection and randomization.) Our universal reference has been developed to represent a wide variety of different samples and ages. The samples used in the reference set have been sourced from many different countries. In our beta tests, the universal reference has performed well in the following countries as of 09/29/2013: USA, UK, France, Germany, and Japan

Answer Id: E13865

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Product FAQ

What are the concentrations of the components in your BrdU Labeling reagent (Cat# 00-0103)?

Answer

Product 00-0103 contains BrdU (5-bromo-2'-deoxyuridine) and FrdU (5-fluoro-2'-deoxyuridine) at a molar ratio of 10:1. The concentrations of BrdU and FrdU in product are approximately 3 mg/mL and 0.3 mg/mL, respectively.

Answer Id: E5133

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Product FAQ

What is the difference between OncoScanCancerGeneOnly.r1 and OncoScanGeneBoundaries.r1?

Answer

OncoScanGeneBoundaries.r1 lists the approximately 900 OncoScan cancer genes and includes greater than 10 kb on each side of the gene. OncoScanCancerGeneOnly.r1 lists the same approximately 900 OncoScan cancer genes using the start and stop positions of the gene (no additional 10 kb on each side of the gene).

Answer Id: E13866

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Product FAQ

Can I see mosaic calls for OncoScan™ data or Genome-Wide Human SNP Array 6.0 data in ChAS 3.1?

Answer

Mosaicism analysis is currently only available for CytoScan™ array files. However, xxCHP files for the other array types contain the SmoothSignal data type, which displays non-integer copy number changes.

Answer Id: E13882

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Product FAQ

Which supplement can I add to Neurobasal™ Medium to culture my neural cells?

Answer

As a general guideline, we recommend using Gibco™ B-27™ Supplement to culture neural stem cells, hippocampal, and other CNS neurons.

- For neuroblastomas, or post-mitotic neurons from both PNS and CNS, Gibco™ N-2 Supplement can be used.
- For primary glial cells (astrocytes) or tumor cell lines of astrocytic phenotype (astrocytes and gliomas), or oligodendrocytes, Gibco™ G-5 Supplement can be used.

Answer Id: E12013

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Product FAQ

What is Thermo Fisher Scientific' Subtraction Probe Technology (SPT)?

Answer

Thermo Fisher Scientific' SPT™ (Subtraction Probe Technology) is a technology that creates specific DNA probes by eliminating the repetitive sequences such as Alu and LINE elements found in the human genome. Consequently, our SPT™ probes are inherently specific and protocols using them do not require extra steps for blocking repetitive sequences. With traditional types of cytogenetic DNA probes, such blocking steps are required. Our SPT™ technology allows identification and evaluation of genetic aberrations under a brightfield microscope using chromogenic detection (CISH). Many more details about our CISH probes can be found on our website in the following section: Products & Services > Diagnostics & Clinical Research, then click on the Anatomical Pathology link at the top right of the page's center section.

Answer Id: E5134

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Product FAQ

Is it possible to use CRISPR-Cas technology for prokaryotic gene engineering?

Answer

Yes, it is possible but our system is not for prokaryotes, and has only been optimized for mammalian systems. Please also consult our CRISPR custom services for further inquiries (custom.services@lifetech.com).

Answer Id: E10132

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Product FAQ

What data files are produced during the assay and analysis process?

Answer

These data files are produced that are key to the process:

ARR file - This file includes sample information.
AUDIT file - This file is a log of the sample history.
DAT file - This file is the raw data from the scanner.
CEL file - This file is the gridded and processed data.
xxCHP file - This file is the output of ChAS 3.1 and contains all of the analysis data.
CHPCAR file - This file stores user-annotated calls, interpretations, and modifications made to CHP file segment data (ChAS v2.0 and higher).

Answer Id: E13867

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Product FAQ

How can I view the histogram data in ChAS 3.1?

Answer

You must be logged into the ChAS database (ChAS DB) to view histogram data. The histograms are only available for NetAffx genomic annotation files for genome build Hg19. The browser produces an error message if you try to load Hg19-based histograms while an Hg18-based NetAffxGenome Annotation is currently displayed.

Answer Id: E13883

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Product FAQ

Can I use the QuantStudio™ 3D Digital PCR Master Mix v2 with the current v1 Chips?

Answer

No, the v2 Master Mix can only be used with the v2 Chips.

Answer Id: E10367

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Product FAQ

Why is the color of Neurobasal™ Medium without Phenol red yellow?

Answer

The yellow color comes from vitamin components.

Answer Id: E12014

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Product FAQ

How does the Luminex™ instrument simultaneously monitor concentrations of several different analytes in a single sample?

Answer

Each protein detected requires a different bead region to differentiate between analytes. The Luminex™ instrument is outfitted with two lasers. The first laser is a red diode laser that classifies beads (region) based on color and hence identifies which protein is being measured. The second laser is a green YAG laser that quantitates reporter fluorophore (R-Phycoerythin, RPE) associated with the bead surface and determines the amount of the protein that is bound to the bead. The beads pass through the system at a rate of several thousand per second, excited first by the red laser and then the green laser. The results obtained show protein identity and the intensity of the signal, respectively. The intensity of the signal is directly proportional to the concentration of the analyte captured in the sample. Therefore, by monitoring the spectral properties of the beads and the amount of associated RPE fluorescence, the concentration of one or more proteins can be determined.

Answer Id: E5135

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Product FAQ

What happens to Cas9 after it performs its endonuclease activity?

Answer

Cas9 is transiently expressed and will therefore disappear over time with successive cell divisions.

Answer Id: E10133

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