GeneScan™ 120 LIZ™ dye Size Standard
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Applied Biosystems™

GeneScan™ 120 LIZ™ dye Size Standard

The GeneScan™ 120 LIZ™ Size Standard is a five dye-labeled size standard that is designed for reproducible sizing of smallRead more
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Catalog NumberQuantity
4324287800 reactions
Catalog number 4324287
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738.00
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800 reactions
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Price (USD)
738.00
Each
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The GeneScan™ 120 LIZ™ Size Standard is a five dye-labeled size standard that is designed for reproducible sizing of small fragment analysis data.

GeneScan™ 120 LIZ™ Size Standard is designed for sizing DNA fragments in the 15-120 nucleotides range and provides nine single-stranded labeled fragment of: 15, 20, 25, 35, 50, 62, 80, 110 and 120 nucleotides. The sizing curve generated from these short fragments make the GeneScan™ 120 LIZ™ Size Standard ideal for use with the ABI Prism SNaPshot™ Multiplex Kit as well as other short fragment analysis applications. Each of the DNA fragments is labeled with the LIZ™ fluorophore which results in a single peak when run under denaturing conditions. With the 5th dye LIZ™ your marker fragments can be labeled with the dyes FAM™, VIC™, NED™ or PET™.

Since the standard is labeled with the fifth dye, you can genotype a greater number of markers in a given lane, compared to the four-dye system.

For Research Use Only. Not for use in diagnostic procedures.
Specifications
Label or DyeLIZ
No. of Reactions800 Reactions
Quantity800 reactions
Shipping ConditionGel Pack
For Use With (Equipment)3730xl DNA Analyzer, 3730 DNA Analyzer, 3500 Series Genetic Analyzers, SeqStudio Flex Series Genetic Analyzers, SeqStudio Genetic Analyzer
Product LineGeneScan, LIZ
TypeDye Size Standard
Unit SizeEach
Contents & Storage
Contains 9 single stranded labeled DNA fragments. Store the kit at 2° to 8°C. (Do not freeze).
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Frequently asked questions (FAQs)

During fragment analysis, the larger peaks of my size standard are missing. Why?

If the larger peaks in the size standard are missing, it can also cause the sizing analysis to fail. This could be sample-related, where smaller ions and PCR products are preferentially injected into the capillaries and out-compete the injection of the larger products. To confirm, the size standard should be run without the sample.

If a size standard-only injection is performed, the larger size standard peaks may be missing due to slower migration of the sample. Slower migration can be due to some of the following:

-Degraded or expired polymer
- Old array or capillary
- Old or incorrect concentration of the buffer
- Old or expired HiDi Formamide
- Colder ambient temperature
- Oven temperature too low
If the issue persists, the instrument run time can be increased in order to allow for longer collection time of the largest size standard peaks. However, if the peak resolution is also broader than expected, this may suggest an instrument issue and a service call should be opened.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

During fragment analysis, I am missing the smaller fragments of my size standard. What happened?

If a size standard-only run is performed and is missing the smaller fragments, degradation of the size standard may have occurred. Please check the expiration date either on the box or the Certificate of Analysis (COA). The size standard should be stored at 4-8 degrees C. Freezing of the size standard will cause loss of the smaller products and may also result in dye breakdown. The size standard should be replaced if expired or stored improperly. If the smaller peaks are missing, they may also be masked by the primer peak. The easiest fix is to go to the GeneMapper Manager, Size Standard tab, select the size standard definition you are working with and click the “Save As” button at the bottom. Rename the new standard and edit it by deleting any size smaller than 50 bp. Click OK, then Done and change the Size Standard in your project and re-analyze the data.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

During fragment analysis, my sample peaks are really strong, but my size standard peaks are really low. Why is this?

If the sample has strong signal and the size standard is weak, the sample may be preferentially injecting into the capillaries. The sample may have a high salt concentration and/or robust amplification. To confirm, a size standard-only sample should be run to confirm the performance of the size standard alone. If the signal intensity improves, the sample may require desalting or less PCR product should be used. If the size standard-only sample still shows low signal, the issue may be with possible degradation of the size standard and it may need to be replaced.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

I am observing "failed sizing" in GeneMapper Software. Why?

In GeneMapper Software, “failed sizing” is a result of the software being unable to identify the size standard peaks as defined by the selected size Standard. Please confirm that the size standard used in the sample matches the size standard selected in GeneMapper Software. The Size Match Editor function in GeneMapper Software allows you to view the size standard peaks sizing assignments. In the Size Match Editor window, the size standard peak heights can be reviewed, the user can determine if all the peaks in the size standard are present, or if there are any extraneous peaks in the same color as the size standard that are present. The Size Match Editor can be accessed by highlighting the failed samples in the Samples tab, and then going to the Analysis pull down menu > Size Match Editor.

-Within the GeneMapper Software's Analysis Method, the Peak Detector tab contains the minimum peak height setting for each color (blue, green, yellow, red, purple, and orange). If the size standard peaks are below the minimum peak height setting on the Y-axis, typically 50, the software will ignore these peaks (this threshold is different for fragment analysis that occurs in the 3500 Data Collection software). Although this setting may be altered, it may be necessary to troubleshoot further before doing so. If the sample has strong signal and the size standard is weak, the sample may be preferentially injecting into the capillaries. The sample may have a high salt concentration and/or robust amplification. To confirm, a size standard-only sample should be run to confirm the performance of the size standard alone. If the signal intensity of the size standard improves, the sample may require desalting or less PCR product should be used. If the size standard-only sample still shows low signal, the issue may be possible degradation of the size standard or the Hi-Di Formamide and they may need to be replaced. It may also be a sign that the capillary array is old or clogged.
-If there are any extraneous peaks, this can be due to pull-up peaks from overloaded samples. Extraneous peaks in the same color as the size standard dye label may interfere with the sizing algorithm in the analysis software. The sample can be reduced to prevent the pull-up peak from overloaded samples. If the sample is not overloaded, please confirm that the fluorescent dye in use is part of the dye set selected. The spectral calibration may also need to be re-run.
- If the larger peaks in the size standard are missing, it can also cause the sizing analysis to fail. This could be sample-related where smaller ions and PCR products are preferentially injected into the capillaries and out-compete the injection of the larger products. To confirm, the size standard should be run without the sample.
- If a size standard-only injection is performed, the larger size standard peaks may be missing due to slower migration of the sample. Slower migration can be due to some of the following:
1.Degraded or expired polymer
2.Old array or capillary
3.Old or incorrect concentration of the buffer
4.Old or expired HiDi Formamide
5.Colder ambient temperature
6.Oven temperature too low
If the issue persists, the instrument run time can be increased in order to allow for longer collection time of the largest size standard peaks. However, if the peak resolution is also broader than expected, this may suggest an instrument issue and a service call should be opened.

- If the smaller peaks in the size standard are missing, they may be masked by the primer peak. The easiest fix is to go to the GeneMapper Manager, Size Standard tab, select the size standard definition you are working with and click the “Save As” button at the bottom. Rename the new standard and edit it by deleting any size smaller than 50 bp. Click OK, then Done and change the size standard in your project and re-analyze the data.

The Size Match Editor will allow overriding of the sample quality but it is important to confirm the size standard peaks are correctly identified. Otherwise, the peak sizes of the PCR products may be shifted. To override the sizing quality in the Size Match Editor, click on the “Override SQ” button on the top, middle of the window.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

I am following a fragment analysis protocol from a publication and my fragment sizes are different using the same control. Why?

- As the size of a fragment is calculated based on the size standard with which it co-migrates, dye-labeled DNA fragments can yield different sizes when run with a different instrument, polymer, capillary array length, or size standard.
- Check to see whether the polymer, buffer, or array has expired and/or is degraded. If so, they will need to be replaced.
- Check that the analysis parameters, analysis method, and size standard selected in the analysis software are the same.
- It is also possible to observe slight shifts in sizing if the lab temperatures differ. This will also impact the migration of the sample.
- If multiple injections of the control yield the same size, then it may be necessary to note the offset in sizes for a given fragment as this will confirm the instrument precision.

Find additional tips, troubleshooting help, and resources within our Capillary Electrophoresis Applications Support Center.

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Notice to Purchaser: This product is optimized for use in the DNA sequencing or fragment analysis methods covered by patents owned and/or controlled by Life Technologies Corporation (“LTC”). LTC does not convey any right or license under these patents, whether expressly, by implication, by estoppels, or otherwise, to the purchaser by the purchase of this product to use the DNA sequencing or fragment analysis methods. Notwithstanding the foregoing, a limited license to use the DNA sequencing or fragment analysis methods covered by such patents can be obtained for certain research and development activities (a) through the purchase of certain LTC reagents when such reagents are used in conjunction with an authorized LTC instrument, or (b) directly from LTC. For information on obtaining additional rights to practice the DNA sequencing or fragment analysis methods, please contact outlicensing@thermofisher.com, Licensing and Commercial Supply, Thermo Fisher Scientific, 5823 Newton Drive, Carlsbad, CA, 92008, United States.

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