Sample Quality

The Agilent 2200 TapeStation and the Invitrogen Qubit provide solutions to quantitate and qualify nucleic acid samples. These services are used to screen both RNA and DNA prior to library preparation performed at the High-Throughput Genomics Shared Resource and the assays are included in the cost associated with library preparation. Researchers may also order these services as stand-alone assays. Product descriptions, frequently Asked Questions and Pricing relevant to these assays are provided below.

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Frequently Asked Questions

Agilent RNA ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is a RIN (RNA Integrity Number)?

The RNA ScreenTape provides a numeric assessment of the integrity of an RNA sample that is reported on a scale between 1 and 10 as a RIN (RNA Integrity Number). The RIN value is therefore used to characterize the quality of the RNA sample and enable direct comparison between different samples. An application note prepared by Agilent that describes the RNA Integrity Number can be reviewed at the following web page: https://www.agilent.com/cs/library/applications/5989-1165EN.pdf


What is the volume and concentration of RNA required for an RNA ScreenTape Assay?

Please provide a volume of 3 ul of purified RNA in water at a concentration of 25-500 ng/ul for samples to be run on an RNA ScreenTape.


Can RNA ScreenTape Assays tolerate contaminants in the RNA Sample?

We recommend purifying RNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute RNA with water. However, the High Sensitivity RNA ScreenTape Assay can tolerate solutions with 10 mM Tris and 1 mM EDTA of 50 mM NaCl.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Agilent High Sensitivity RNA ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is a RIN (RNA Integrity Number)?

The RNA ScreenTape provides a numeric assessment of the integrity of an RNA sample that is reported on a scale between 1 and 10 as a RIN (RNA Integrity Number). The RIN value is therefore used to characterize the quality of the RNA sample and enable direct comparison between different samples. An application note prepared by Agilent that describes the RNA Integrity Number can be reviewed at the following web page: https://www.agilent.com/cs/library/applications/5989-1165EN.pdf


What is the volume and concentration of RNA required for a High Sensitivity RNA ScreenTape Assay?

Please provide a volume of 3 ul of purified RNA in water at a concentration of 1-25 ng/ul for samples to be run on a High Sensitivity RNA ScreenTape.


Can RNA ScreenTape Assays tolerate contaminants in the RNA Sample?

We recommend purifying RNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute RNA with water. However, the High Sensitivity RNA ScreenTape Assay can tolerate solutions with 10 mM Tris and 1 mM EDTA.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Agilent D1000 ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is the volume and concentration of DNA required for a D1000 ScreenTape Assay?

Please provide a volume of 3 ul of purified DNA at a concentration of 2-50 ng/ul for samples to be run on a D1000 ScreenTape.


What is the size distribution of DNA that can be resolved on a D1000 ScreenTape Assay?

The D1000 ScreenTape has a sizing range of 35-1000 bp. However, the most accurate sizing resolution lies between 300 and 1000 bp.


Can D1000 ScreenTape Assays tolerate contaminants in the sample?

We recommend purifying DNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute the DNA in 10 mM Tris pH 8.5. However, A D1000 ScreenTape can tolerate 20 mM KCl, 60 mM Phosphate Buffer, or 240 mM NaCl. The DNA may exhibit an anomalous size distribution if the sample is not purified and provided in an enzyme reaction buffer (pcr reaction, restriction enzyme reaction, etc.).


Can Single-Stranded DNA be accurately resolved on a D1000 ScreenTape?

Single-stranded DNA tends to run with a lower mobility (higher apparent MW) than expected when resolved on a D1000 ScreenTape. Over-amplification of sequencing libraries may result in a substantial fraction of single-stranded DNA may exhibit two distinct peaks- -one of the appropriate size distribution that represents double-stranded DNA and a second peak that represents single-stranded DNA that is inaccurately resolved at an apparent higher molecular weight.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Agilent High Sensitivity D1000 ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is the volume and concentration of DNA required for a High Sensitivity D1000 ScreenTape Assay?

Please provide a volume of 3 ul of purified DNA at a concentration of 0.01 to 1 ng/ul for samples to be run on a High Sensitivity D1000 ScreenTape.


What is the size distribution of DNA that can be resolved on a High Sensitivity D1000 ScreenTape?

The High Sensitivity D1000 ScreenTape has a sizing range of 35-1000 bp. However, the most accurate sizing resolution lies between 300 and 1000 bp.


Can High Sensitivity D1000 ScreenTape Assays tolerate contaminants in the sample?

We recommend purifying DNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute the DNA in 10 mM Tris pH 8.5. However, A High Sensitivity D1000 ScreenTape can tolerate 7 mM KCl, 20 mM Phosphate Buffer, or 80 mM NaCl. The DNA may exhibit an anomalous size distribution if the sample is not purified and provided in an enzyme reaction buffer (pcr reaction, restriction enzyme reaction, etc.).


Can Single-Stranded DNA be accurately resolved on a High Sensitivity D1000 ScreenTape?

Single-stranded DNA tends to run with a lower mobility (higher apparent MW) than expected when resolved on a High Sensitivity D1000 ScreenTape. Over-amplification of sequencing libraries may result in a substantial fraction of single-stranded DNA may exhibit two distinct peaks- -one of the appropriate size distribution that represents double-stranded DNA and a second peak that represents single-stranded DNA that is inaccurately resolved at an apparent higher molecular weight.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Agilent High Sensitivity D5000 ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is the volume and concentration of DNA required for a High Sensitivity D5000 ScreenTape Assay?

Please provide a volume of 3 ul of purified DNA at a concentration of 0.01 to 1 ng/ul for samples to be run on a High Sensitivity D1000 ScreenTape.


What is the size distribution of DNA that can be resolved on a High Sensitivity D5000 ScreenTape?

The High Sensitivity D5000 ScreenTape has a sizing range of 100-5000 bp. However, the most accurate sizing resolution lies between 400 and 5000 bp.


Can High Sensitivity D5000 ScreenTape Assays tolerate contaminants in the sample?

We recommend purifying DNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute the DNA in 10 mM Tris pH 8.5. However, A High Sensitivity D5000 ScreenTape can tolerate 25 mM KCl or 12.5 mM NaCl. The DNA may exhibit an anomalous size distribution if the sample is not purified and provided in an enzyme reaction buffer (pcr reaction, restriction enzyme reaction, etc.).


Can Single-Stranded DNA be accurately resolved on a High Sensitivity D5000 ScreenTape?

Single-stranded DNA tends to run with a lower mobility (higher apparent MW) than expected when resolved on a High Sensitivity D5000 ScreenTape. Over-amplification of sequencing libraries may result in a substantial fraction of single-stranded DNA may exhibit two distinct peaks- -one of the appropriate size distribution that represents double-stranded DNA and a second peak that represents single-stranded DNA that is inaccurately resolved at an apparent higher molecular weight.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Agilent Genomic DNA ScreenTape Assay

How does an Agilent ScreenTape assay work?

Agilent ScreenTapes contain a gel matrix to resolve nucleic acid samples according to molecular weight by electrophoresis.


What is the volume and concentration of DNA required for a Genomic DNA ScreenTape Assay?

Please provide a volume of 3 ul of purified DNA at a concentration of 10-200 ng/ul for samples to be run on a Genomic DNA ScreenTape.


What is the size distribution of DNA that can be resolved on a Genomic DNA ScreenTape?

The Genomic DNA ScreenTape has a sizing range of 200 to 60,000 bp. However, the most accurate sizing resolution lies between 200 and 15,000 bp.


Can Genomic DNA ScreenTape Assays tolerate contaminants in the sample?

We recommend purifying DNA with spin-column based purification kits (Qiagen, Zymo Research etc.) that elute the DNA in 10 mM Tris pH 8.5. However, A D1000 ScreenTape can tolerate 50 mM NaCl, 10 mM MgCl2, or 50 mM NaAc. The DNA may exhibit an anomalous size distribution if the sample is not purified and provided in a cell lysis reaction mixture.


How do I obtain data from a TapeStation assay?

TapeStation data can be obtained by browsing to the Experiment Folder in GNomEx. Click on the “Files” tab and open the “Sample QC” folder and select the files that you would like to download.

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Invitrogen Qubit dsDNA HS Assay

What is the volume and concentration of DNA required for a Qubit dsDNA HS Assay?

Please provide a volume of 3 ul of purified DNA at a concentration of 0.05 to 100 ng/ul for the Qubit dsDNA High Sensitivity Assay.


Is the Qubit dsDNA HS Assay more accurate than a NanoDrop reading for the measurement of DNA concentration?

A NanoDrop spectrophotometer is unable to distinguish between DNA, RNA, oligonucleotides, free nucleotides and other nucleic acid species. An A260 measurement on a NanoDrop represents any form of nucleotide. In contrast to a NanoDrop reading, the Qubit dsDNA High Sensitivity Assay uses a dye that is highly selective for binding double-stranded DNA and therefore is able to accurately determine DNA concentrations in the presence of RNA or other nucleic acid species which can comprise a substantial fraction of many samples.


Can I purchase Qubit reagents and tubes to measure my samples on a Qubit instrument at the High-Throughput Genomic Shared Resource?

A version 2 Qubit instrument is available in the entryway of the High-Throughput Genomics Shared Resource that can be used by researchers that have purchased their own Qubit reagents and Qubit tubes. This instrument can be used for the following assays: Qubit dsDNA HS Assay, Qubit dsDNA BR Assay, Qubit RNA BR Assay.


How do I obtain data from a Qubit assay?

Data from Qubit assays will be entered into GNomEx and sample concentrations can be reviewed by navigating to your GNomEx experiment folder.

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Invitrogen Qubit RNA BR Assay

What is the volume and concentration of RNA required for a Qubit RNA BR Assay?

Please provide a volume of 3 ul of purified RNA at a concentration of 5 to 500 ng/ul for the Qubit RNA Broad Range Assay.


Is the Qubit RNA BR Assay more accurate than a NanoDrop reading for the measurement of DNA concentration?

A NanoDrop spectrophotometer is unable to distinguish between DNA, RNA, oligonucleotides, free nucleotides and other nucleic acid species. An A260 measurement on a NanoDrop represents any form of nucleotide. In contrast to a NanoDrop reading, the Qubit RNA BR Assay uses a dye that is highly selective for binding RNA and is therefore able to accurately measure RNA concentrations in the presence of DNA or other nucleic acid species.


Can I purchase Qubit reagents and tubes to measure my samples on a Qubit instrument at the High-Throughput Genomic Shared Resource?

A version 2 Qubit instrument is available in the entryway of the High-Throughput Genomics Shared Resource that can be used by researchers that have purchased their own Qubit reagents and Qubit tubes. This instrument can be used for the following assays: Qubit dsDNA HS Assay, Qubit dsDNA BR Assay, Qubit RNA BR Assay.


How do I obtain data from a Qubit assay?

Data from Qubit assays will be entered into GNomEx and sample concentrations can be reviewed by navigating to your GNomEx experiment folder.

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Invitrogen Qubit RNA HS Assay

What is the volume and concentration of RNA required for a Qubit RNA HS Assay?

Please provide a volume of 3 ul of purified RNA at a concentration of 0.10 to 50 ng/ul for the Qubit RNA High Sensitivity Assay.


Is the Qubit dsDNA HS Assay more accurate than a NanoDrop reading for the measurement of DNA concentration?

A NanoDrop spectrophotometer is unable to distinguish between DNA, RNA, oligonucleotides, free nucleotides and other nucleic acid species. An A260 measurement on a NanoDrop represents any form of nucleotide. In contrast to a NanoDrop reading, the Qubit RNA HS Assay uses a dye that is highly selective for binding RNA and is therefore able to accurately measure RNA concentrations in the presence of DNA or other nucleic acid species.


Can I purchase Qubit reagents and tubes to measure my samples on a Qubit instrument at the High-Throughput Genomic Shared Resource?

A version 2 Qubit instrument is available in the entryway of the High-Throughput Genomics Shared Resource that can be used by researchers that have purchased their own Qubit reagents and Qubit tubes. This instrument can be used for the following assays: Qubit dsDNA HS Assay, Qubit dsDNA BR Assay, Qubit RNA BR Assay.


How do I obtain data from a Qubit assay?

Data from Qubit assays will be entered into GNomEx and sample concentrations can be reviewed by navigating to your GNomEx experiment folder.

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Contact Us

High-Throughput Genomics Director
Brian K. Dalley, PhD
brian.dalley@hci.utah.edu
801-585-7192

Governance

HCI Senior Director Oversight
Alana Welm, PhD

Faculty Advisory Committee Chair
Katherine Varley, PhD

Faculty Advisory Committee Members
Richard Clark, PhD
Jason Gertz, PhD
Christopher Gregg, PhD
Mei Koh, PhD
Philip Moos, PhD
Andrew Post, MD, PhD
Sean Tavtigian, PhD
Joseph Yost, PhD