Fragment Analyzer

Introducing one powerful instrument to cover the full spectrum of DNA, gDNA and RNA quality control. The Fragment Analyzer™ Automated CE System does everything from high-resolution analysis to fast DNA separations, across the widest separation range.

AATI Scientist looking at data

Fragment Analyzer Application Notes

Benefits of Quality Control in the IVT RNA Workflow

Published:Wednesday, August 8th, 2018

Quality control (QC) analysis is an essential part of the in vitro transcription (IVT) RNA workflow. Utilizing QC checkpoints at critical junctures in the IVT RNA process eliminates unsuitable samples, saves time and money, and maximizes resources. The Fragment Analyzer™ Automated CE System from Advanced Analytical - A part of Agilent provides sensitive and reliable quality control analysis of RNA with the DNF-471 Standard Sensitivity RNA Analysis Kit and DNF-472 High Sensitivity RNA Analysis Kit and analysis of DNA with a variety of DNA Kits. QC during IVT allows for detection of poor PCR amplification, poor transcription, DNA template contamination of RNA, degraded RNA, and ensures downstream applications are starting with high-quality RNA.

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Analysis of In Vitro Transcribed Cas9 mRNA Pre- and Post-Polyadenylation

Published:Wednesday, August 8th, 2018

DNA-free CRISPR gene editing has become a popular way to control for off-target effects during CRISPR transfection, however the size of the Cas9 protein does not always allow for transfection of Cas9/sgRNA ribonucleoprotein complexes. A way to overcome this method of DNA-free CRISPR gene editing is to transfect both in vitro transcribed sgRNA and Cas9 mRNA. Polyadenylation (poly(A)) of the Cas9 mRNA allows for a longer translation time by protecting and increasing the stability of the Cas9 transcript. The Fragment Analyzer™ Automated CE System from Advanced Analytical Technologies, Inc. (AATI) coupled with the DNF-472 High Sensitivity RNA Analysis Kit provides high-resolution separation and consistent sizing of the Cas9 mRNA with or without polyadenylation.

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Quality Analysis of Eukaryotic Total RNA with the Fragment Analyzer

Published:Thursday, May 31st, 2018

Advanced Analytical Technologies, Inc.'s Fragment Analyzer™ Automated CE System and associated RNA Kits allow for easy and reliable analysis of RNA quality and concentration. PROSize® Data Analysis Software provides an electropherogram and a digital gel image for visual inspection of RNA. In addition, PROSize automatically reports the concentration, ribosomal ratio, and assigns an RNA Quality Number (RQN). The Fragment Analyzer delivers consistent and reliable RNA concentration measurements and RQN values between instruments and throughout the RNA dilution series.

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Best Sizing Practices for the Fragment Analyzer

Published:Thursday, May 31st, 2018

Quality control check points for sizing are a necessity for library preparation. Accurate sizing ensures successful library preps and downstream sequencing. The Fragment Analyzer Automated CE System from Advanced Analytical Technologies, Inc. (AATI) provides reliable sizing for fragments and smears with PROSize® Data Analysis Software. This application note describes factors that affect sizing and the best practices for achieving accurate sizing of the sample.

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Best Quantification Practices for the Fragment Analyzer

Published:Thursday, May 31st, 2018

Quality control check points for concentration are a necessity for library preparation. Accurate concentration ensures successful library preps and downstream sequencing. The Fragment Analyzer Automated CE System from Advanced Analytical Technologies, Inc. (AATI) provides reliable quantification for fragments and smears with PROSize® Data Analysis Software. This application note describes factors that affect quantification and the best practices for achieving accurate quantification of the sample.

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Assessment of Genomic DNA quality with DNF-467 and DNF-468 with the Fragment Analyzer

Published:Friday, May 11th, 2018

The successful outcome of techniques such as next-generation sequencing (NGS) rely on the quality of genomic DNA (gDNA) starting material. Advanced Analytical Technologies, Inc.'s (AATI) Fragment Analyzer Automated CE System offers effortless analysis of genomic DNA (gDNA) with the DNF-467 Genomic DNA 50Kb Analysis Kit and the DNF-468 High Sensitivity Genomic DNA 50Kb Analysis Kit. gDNA up to 60,000 bp in size and over a wide concentration range can be analyzed with both Kits. PROSize® Data Analysis Software provides an electropherogram and a digital gel image for easy visual inspection and assigns a Genomic Quality Number (GQN) for quick evaluation of gDNA quality. The Fragment Analyzer, equipped with the short or ultra-short array offers consistent sizing, quantification, and GQN assessment of gDNA with both the DNF-467 and DNF-468 Kits.

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Quality Metrics

Published:Tuesday, April 3rd, 2018

Advanced Analytical Technologies, Inc. (AATI) uses four quality metrics, the DQN, GQN, RQN, and DV200 to assess the quality and integrity of DNA and RNA. These metrics have been published in numerous articles and incorporated in protocols and literature by Illumina®, PacBio®, and Bionano Genomics®.

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Analysis of Long ssDNA for Use CRISPR/Cas HDR

Published:Tuesday, March 27th, 2018

Single stranded DNA (ssDNA) templates are becoming increasingly useful in CRISPR/Cas homology directed repair (HDR). Analysis of ssDNA prepared from digestion of dsDNA was compared on the Fragment Analyzer&8482; Automated CE System from Advanced Analytical Technologies, Inc. and agarose gel electrophoresis. The high sensitivity and resolution of the Fragment Analyzer allowed for detection of small amounts of undigested dsDNA not detectable on the agarose gel.

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Highly Resolved Separation of DNA Fragments on the Fragment Analyzer

Published:Firday, December 15th, 2017

Complete analysis of PCR amplicons requires an instrument capable of delivering reliable sizing and quality control parameters. Advanced Analytical Technologies, Inc.’s (AATI) Fragment Analyzer™ Automated CE System with the DNF-905 dsDNA 905 Reagent Kit, 1 bp - 500 bp and DNF-477 High Sensitivity Small Fragment Analysis Kit offers exceptional quantification, qualification, and separation of known DNA fragment sizes with a 3-base pair difference.

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Use of an Engineered Restriction Site to Estimate CRISPR Homology Directed Repair Efficiency

Published:Wednesday, April 19th, 2017

The Fragment Analyzer™ Automated CE System from Advanced Analytical Technologies, Inc. (AATI), coupled with the DNF-910CP CRISPR Gel Discovery Kit, provides high-throughput analysis for detection of CRISPR induced Homology Directed Repair (HDR) knock-in of novel restriction enzyme sites. The presented method allows for determination of the approximate frequency of HDR repairs in both pooled and individual cell line systems when utilizing CRISPR gene editing.

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Comparison of DNF-474 and DNF-477 on the Fragment Analyzer with the Short and Ultra-Short Array

Published:Wednesday, April 5th, 2017

Advanced Analytical Technologies, Inc.'s (AATI) Fragment AnalyzerTM Automated CE System offers easy analysis of sheared genomic DNA (gDNA) smears and libraries with the DNF-474 High Sensitivity NGS Fragment Analysis Kit and the DNF-477 High Sensitivity Small Fragment Analysis Kit. PROSize® Data Analysis Software provides an electropherogram and a digital gel image for visual inspection of smear quality and automaticallyreports smear size and concentration. The Fragment Analyzer equipped with the short or ultra-short array offers consistent sizing and quantification of gDNA smears with both Kits.

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Plant RNA Degradation Detection with the Fragment Analyzer

Published:Wednesday, April 5th, 2017

Assessment of RNA quality is a critical component in the success of genomic techniques such as RT-PCR, microarray analysis, and next-generation sequencing (NGS). Advanced Analytical Technologies, Inc.'s (AATI) Fragment AnalyzerTM Automated CE System and associated RNA Kits allow for easy analysis of RNA quality. The PROSize® Data Analysis Software provides an electropherogram and a digital gel image for visual inspection, automatically reports the ribosomal ratio, and assigns an RNA Quality Number (RQN) for total RNA to every sample. PROSize includes a dedicated plant mode for evaluating complex plant RNA. Here, we demonstrate the ease of assessing plant RNA integrity with excellent RQN precision on the Fragment Analyzer.

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Heteroduplex Cleavage Assay for Screening of Probable Zygosities Resulting from CRISPR Mutations

Published:Friday, March 31th, 2017

The most commonly used method of gene editing is the random repair of the double stranded break through the non-homologous end joining pathway which results in small insertions/deletions. In diploid cells these mutations can take on one of three zygosities: monoallelic, diallelic heterozygous, or diallelic homozygous. While many advances have been made to CRISPR delivery systems and gene editing efficiency, little work has been done to streamline the detection of gene editing events.

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Single Guide RNA Quality Assessment By Fragment Analyzer

Published:Monday, January 23th, 2017

One method of CRISPR/Cas9 gene editing is the delivery of Cas9 complexed in vitro with a single guide RNA (sgRNA). Traditionally, quality control analysis of sgRNA prior to Cas9 complexing is performed by agarose gel electrophoresis. The Fragment AnalyzerTM Automated CE System by Advanced Analytical Technologies Inc. (AATI), offers easy visual quality assessment of sgRNA integrity with excellent separation of the linear and secondary structure fragments on both the DNF-472 High Sensitivity RNA Analysis Kit, 15nt and the DNF-470 Small RNA Analysis Kit. Reliable parallel capillary electrophoresis with the Fragment Analyzer provides consistent quantification and sizing for each sgRNA sample.

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Accurate QC Analysis of cfDNA with the Fragment Analyzer

Published:Wednesday, December 14th, 2016

Circulating cell-free DNA (cfDNA) is gaining prevalence as a non-invasive, alternative approach for the detection of tumor mutations in cancer management (1) and screening tests for fetal abnormalities from the mother's blood (2). cfDNA is known to circulate in healthy and pathological conditions and is present in plasma, serum, cerebral spinal fluid, and saliva. Evidence has suggested that highly fragmented cfDNA is actively secreted when new nucleic acids are synthesized and passively released as an end product of necrosis and apoptotic cell death (1).

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Separations of cfDNA with DNF-474 by the Fragment Analyzer Short and Ultra-Short Array

Published:Wednesday, December 14th, 2016

Circulating cell-free DNA (cfDNA) is gaining prevalence as a non-invasive, alternative approach for the detection of tumor mutations (1) and screen for fetal abnormalities from the mother's blood (2). Quantification and assessment of cfDNA and contaminating DNA is necessary for both preparation and quality control of cfDNA generated NGS libraries. The capability of DNF-474 High Sensitivity NGS Fragment Analysis Kit to separate cfDNA on the Fragment Analyzer Automated CE System was investigated.

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