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

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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Quality Analysis of cfDNA with the Fragment Analyzer™ in Comparison with Another Electrophoresis System

Published: Wednesday, April 19th, 2017

Quantification and assessment of cell-free DNA (cfDNA) is necessary for both preparation and quality control of cfDNA generated Next-Generation Sequencing (NGS) libraries and detection of mutation markers. The Fragment Analyzer™ Automated CE System from Advanced Analytical Technologies, Inc. (AATI) provides a high-resolution separation of cfDNA fragments, consistent fragment sizing, and quantification. Analysis of cfDNA by AATI's Fragment Analyzer was compared to the Bioanalyzer® 2100.

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

Published: Wednesday, April 5th, 2017

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 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 AnalyzerTM Automated CE System from Advanced Analytical Technologies, Inc. (AATI) coupled with the DNF-472 High Sensitivity RNA Analysis Kit provides a high-resolution separation and consistent sizing of the Cas9 mRNA with or without polyadenylation. Analysis of Cas9 mRNA with and without polyadenylation by AATI's Fragment Analyzer was compared to the Bioanalyzer® 2100 and the 2200 TapeStation System.

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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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Streamline your ChIP-seq workflow with Diagenode and AATI

Published: Monday, March 20th, 2017

Combined chromatin immunoprecipitation and next-generation sequencing (ChIP-seq) has become the gold standard to investigate genome-wide epigenetic profiles. However, ChIP from a limited amount of cells has been a challenge. Diagenode and Advanced Analytical Technologies, Inc. (AATI) provide the first complete and robust workflow solution for successful ChIP-seq from small numbers of cells.

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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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