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Parallel capillary electrophoresis system used for nucleic acid QC in low- to medium-throughput labs.
This document includes system overviews, analytical methods, maintenance procedures, software operation, troubleshooting guide, and instrument shutdown procedures.
- Publication Part Number: D0002110
- Created: 24 July 2026
- 8 MB
| Spanish (United States) | Complete (PDF) |
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| German (United States) | Complete (PDF) |
| Dutch (United States) | Complete (PDF) |
| French (United States) | Complete (PDF) |
| Italian (United States) | Complete (PDF) |
This technical overview details the different methods available for the analysis of IVT RNA using the HS RNA kit on the Fragment Analyzer.
- Publication Part Number: 5994-7644en
- Created: 01 Sep 2025
- 883 KB
This application note provides an example of a suitability study using the Agilent Fragment Analyzer system.
- Publication Part Number: 5994-8480EN
- Created: 02 July 2025
- 751 KB
This technical overview provides examples of CQAs for IVT mRNA, such as size, concentration, purity, and integrity, that can be addressed by the Agilent Fragment Analyzer system.
- Publication Part Number: 5994-8171EN
- Created: 05 Mar 2025
- 382 KB
Fragment Analyzer
Fragment Analyzer
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Product Updates: Product Obsolescence Notice New methods for IVT mRNA analysis using the HS RNA kit Discontinuation of Legacy Fragment Analyzer Kit in 2023 User Manuals and Videos Title Type Fragment Analyzer User Manual Recommended PC setup (page 11) Capillary Alignment (page 52) Capillary Array Removel & Installation (page 94) Preventative Maintenance Schedule (page 144) Capillary Array Cleaning (page 145) Capillary Array Window Cleaning (page 152) User Manual ProSize Data Analysis Software Manual User Manual Capillary Array Installation on Parallel Capillary Electrophoresis Instruments Knowledge Portal Article How it works: Operation of the Agilent Fragment Analyzer systems Video Video Capillary Array Installation on Fragment Analyzer systems video Video Collecting Troubleshooting information - Event, Error reports and Zipped data folder Instruction Guide Steps for Long- term Instrument Storage Knowledge Portal Article Syringe Replacement Knowledge Portal Article Quick Guides Title Type DNF-464 HS Large Fragment Kit Quick Guide DNF-492 Large Fragment Kit Quick Guide DNF-467 Genomic DNA 50 kb Kit Quick Guide DNF-468 HS Genomic DNA 50 kb Kit Quick Guide DNF-488 HS Genomic DNA Kit Quick Guide DNF-473 NGS Fragment Kit Quick Guide DNF-474 HS NGS Fragment Kit Quick Guide DNF-476 Small Fragment Kit Quick Guide DNF-477 HS Small Fragment Kit Quick Guide DNF-905 Reagent Kit Quick Guide DNF-935 Reagent Kit Quick Guide DNF-910 Reagent Kit Quick Guide DNF-915 Reagent Kit Quick Guide DNF-920 Reagent Kit Quick Guide DNF-930 Reagent Kit Quick Guide DNF-940 Plasmid DNA Kit Quick Guide DNF-470 Small RNA Kit Quick Guide DNF-471 RNA Kit - Total RNA Quick Guide DNF-471 RNA Kit - IVT mRNA Quick Guide DNF-472 HS RNA Kit - Total RNA Quick Guide DNF-472 HSRNA - IVT mRNA Quick Guide Application Resources and Technical Notes Title Description Type Reliable Results for Nucleic Acid Analysis. Agilent 5200, 5300, and 5400 Fragment Analyzer Systems Nucleic acid analysis using Fragment Analyzer Systems Brochure Build Consistency into Your Lab’s Workflow with the Agilent Automated Electrophoresis Portfolio Automated Electrophoresis Portfolio Brochure Quality Control of Nucleic Acids: Best Practices for Biobanks and Biorepositories DNA & RNA White Paper Research Citation Collection Selected publications featuring Agilent Automated Electrophoresis instruments for infectious disease research DNA & RNA Research Citation Collection Nucleic Acid Analysis for Sample Quality Assessment Using the Agilent Fragment Analyzer Systems DNA & RNA Application Compendium Quality Metrics for Nucleic Acids with the Agilent Fragment Analyzer and Femto Pulse Systems DNA & RNA Application Note Sample Quality Control in Next-Generation Sequencing Workflows Application compendium DNA & RNA Application Compendium The Importance of Quality Control in NGS Preparation Workflows: A Review of Applications using the Agilent Automated Electrophoresis Portfolio DNA & RNA White Paper Quality Control Steps for Viral Detection and Sequencing DNA & RNA White Paper Pioneering Advanced Nucleic Acid Analysis for Gene and Cell Therapy Development at TATAA Biocenter DNA & RNA Case Study Accurate QC Analysis of cfDNA Using the Agilent 5200 Fragment Analyzer System DNA Application Note Quality Control of Magnis SureSelect XT HS Workflow with Agilent Automated Electrophoresis Solutions DNA Application Note Quality Control of NGS Libraries with Daisy Chains DNA Application Note Comparison of DNA Sample QC for NGS Workflows for the Agilent Fragment Analyzer and Bioanalyzer Systems DNA Technical Overview Separation Resolution Capabilities of the Agilent ZAG 135 and 110 dsDNA Kits and the Agilent Fragment Analyzer dsDNA 935 and 915 Reagents Kits DNA Technical Overview Comparison of the Agilent ZAG DNA Analyzer and Agilent Fragment Analyzer Systems DNA Technical Overview Preventive Control of Sequencing Through the Insert with the Agilent 5200 Fragment Analyzer System DNA Application Note Plasmid Analysis Using the Agilent Fragment Analyzer Systems DNA Technical Overview Quality Assessment of NGS Libraries using Agilent Automated Electrophoresis Systems DNA Technical Overview Comparison of Small DNA Fragment Analysis using the Agilent Bioanalyzer and Agilent Fragment Analyzer Systems DNA Technical Overview Detection of Adapter Dimers in NGS Libraries with the Agilent Fragment Analyzer and TapeStation Systems DNA Technical Overview Comparison of Constant- and PulsedField Electrophoresis Technologies for Analysis of High Molecular Weight and Large DNA Fragments DNA Application Note Target Capture Long-Read Sequencing Using the Agilent SureSelect XT HS2 Target Enrichment System DNA Application Note Fragment Analysis Research Citation Collection Selected publications featuring the Agilent Fragment Analyzer DNA Research Citation Collection Best Sizing Practices with the Agilent 5200 Fragment Analyzer System DNA Application Note Best Quantification Practices with the Agilent 5200 Fragment Analyzer System DNA Application Note Separation of cfDNA with the Agilent HS NGS Kit on the Agilent Fragment Analyzer Systems DNA Application Note Highly Resolved Separation of DNA Fragments on the Agilent 5200 Fragment Analyzer System DNA Application Note Assessment of Genomic DNA Quality with the Agilent 5200 Fragment Analyzer System DNA Application Note Comparison of HS Small Fragment Kit and HS NGS Fragment Kit on the Agilent 5200 Fragment Analyzer System DNA Application Note Quality Control in the PacBio HiFi Whole Genome Sequencing Library Preparation Workflow Genomics Application Note Suitability Testing for IVT mRNA Analysis Using Agilent Fragment Analyzer Systems Genomics Application Note Analysis of in Vitro Transcribed Cas9 mRNA Pre- and Post-polyadenylation with the Agilent 5200 Fragment Analyzer System RNA Application Note Comparison of RIN and RQN for the 2100 Bioanalyzer and the 5200 Fragment Analyzer Systems RNA Technical Overview A Review of RNA Analysis using the Agilent Automated Electrophoresis Portfolio RNA White Paper Comparison of Small RNA Analysis using the Agilent Bioanalyzer and Agilent Fragment Analyzer Systems RNA Technical Overview Analyzing Poly(A) Tails of In Vitro Transcribed RNA with the Agilent Fragment Analyzer System RNA Application Note Comparison of RNA Quality Analysis with the Qubit RNA IQ Assay and Agilent Automated Electrophoresis Systems RNA Technical Overview Comparison of the Agilent 2100 Bioanalyzer and the Agilent Fragment Analyzer Systems for Analysis of Plant, Insect, and Bacterial RNA RNA Technical Overview Best Practices for Analysis of In Vitro Transcribed (IVT) mRNA Using the Agilent Fragment Analyzer systems RNA Technical Overview Best Practices for Analysis of IVT mRNA Using the Agilent Fragment Analyzer systems - Sizing, Resolution, and Purit y RNA Technical Overview RNA Quality Assessment with the Agilent Automated Electrophoresis Systems RNA Technical Overview High-Sensitivity IVT mRNA Analysis Using the Agilent Fragment Analyzer Systems RNA Technical Overview CQA Assessment of LNP-Encapsulated IVT mRNA Using Agilent Fragment Analyzer Systems RNA Technical Overview IVT mRNA Encapsulation Efficiency Assessment Using Agilent Fragment Analyzer Systems RNA Application Note FFPE RNA Quality Assessment with the Agilent Bioanalyzer and Fragment Analyzer Systems RNA Technical Overview From Start to Finish: Agilent CQA Analysis Solutions for IVT mRNA-based Biotherapeutics RNA Application Compendium Quality Analysis of Eukaryotic Total RNA with the Agilent 5200 Fragment Analyzer System RNA Application Note Plant RNA Degradation Detection Using the Agilent 5200 Fragment Analyzer System RNA Application Note Benefits of Quality Control in the IVT RNA Workflow Using the Agilent 5200 Fragment Analyzer System RNA Application Note Assessment of Long IVT mRNA Fragments with the Agilent 5200 Fragment Analyzer system RNA Application Note Quality Assurance in In Vitro Transcribed (IVT) RNA Vaccine Development using Agilent Automated Electrophoresis Instruments RNA White Paper Software Title Description Software Download for Agilent Fragment Analyzer Systems Fragment Analyzer Controller Software Revision 5.0.0 Agilent ProSize Data Analysis Software Revision 6.0.0 ProSize Data Analysis Software Tutorial Videos Software ReadMe files FFPE DV200 Calculation Method/Configuration File IVT mRNA Extended Separation Method/Configuration File Small Fragment Method/Configuration File Software Download for Agilent Fragment Analyzer Systems | Security Module Single package consisting of: Administration Software revision 1.0.0 Fragment Analyzer controller software revision 5.0.0 ProSize data analysis software revision 6.0.0.
ProSize tutorial video no sound
ProSize tutorial video no sound
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https://www.agilent.com/en/product/automated-electrophoresis/fragment-analyzer-systems/fragment-analyzer-systems-software/how-to-videos-for-prosize-data-analysis-software The Prosize tutorial videos have no sound, could you please fix it or direct me to were I can find the videos with sound? The ones in my computer that comes with 5200 also have no sound.
dsRNA analysis on Fragment Analyzer
dsRNA analysis on Fragment Analyzer
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Hi everyone! Does anybody know how to visualize dsRNA fragments correctly on Fragment Analyzer? We have 800bp and 500bp sizes for our dsRNA, confirmed by traditional agarose electrophoresis. However, that's not what we see in CE: 1) On our DNA 35-1500bp gel, we see them as 500bp and 300bp respectively. 2) On RNA (HS RNA 15nt kit), we see them higher, on 2.6Kb and 920bp respectively. We're running out of ideas, so if somebody has any experience checking dsRNA on Fragment Analyzer, I'd appreciate a tip about this issue. Thanks!
Frozen blank solution of the fragment analyzer
Frozen blank solution of the fragment analyzer
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Hi community, I mistakenly froze the fragment analyzer's blank solution (DNF-300-0008) once at -20°C for about 4 hours. Is there any way to rescue it?
This application note uses the Fragment Analyzer and HS RNA kit and provides an example of the calculation of encapsulation efficiency by quantifying IVT mRNAs before and after LNP disruption.
- Publication Part Number: 5994-8036EN
- Created: 20 Feb 2025
- 494 KB
The compendium showcases Agilent Fragment Analyzer, TapeStation, 1290 Infinity Bio LC, and 6545 XT Advance Bio LC/Q-TOF systems in IVT mRNA biotherapeutics workflow.
- Publication Part Number: 5994-7961EN
- Created: 01 Nov 2024
- 16 MB
In this technical overview, best practices for analysis of IVT mRNA are discussed, with particular attention to the use of the Agilent RNA kit and Fragment Analyzer systems.
- Publication Part Number: 5994-6568EN
- Created: 07 Sep 2023
- 1 MB
The Agilent 5200 Fragment Analyzer provides sensitive, reliable quality control analysis of RNA in the in vitro transcription (IVT) RNA workflow.
- Publication Part Number: 5994-0512EN
- Created: 05 July 2023
- 914 KB
This technical overview discusses best handling practices for IVT mRNA and analysis with the Fragment Analyzer systems, including sample handling and quantification tips.
- Publication Part Number: 5994-5927EN
- Created: 17 May 2023
- 947 KB
This application note describes the procedures necessary to obtain reliable sizing for poly(A) tails using the Fragment Analyzer.
- Publication Part Number: 5994-5325EN
- Created: 13 Sep 2022
- 602 KB
The use of in vitro transcription (IVT) mRNA is becoming widespread in research areas such as ribozyme and aptamer synthesis, mRNA synthesis, RNA interference, and antisense RNA techniques. Longer RNA transcripts greater than 3,000 nt are needed for...
- Publication Part Number: 5994-0878EN
- Created: 25 June 2020
- 955 KB
The Agilent Fragment Analyzer and associated RNA Kits allow for easy analysis of RNA quality in RT-PCR, microarray analysis, and next-generation sequencing.
- Publication Part Number: 5994-0518EN
- Created: 18 Feb 2019
- 2 MB
The Agilent 5200 Fragment Analyzer and associated RNA Kits allow for easy analysis of total RNA quality and concentration.
- Publication Part Number: 5994-0519EN
- Created: 18 Feb 2019
- 3 MB
The Agilent 5200 Fragment Analyzer system provides high resolution separation and consistent sizing of the Cas9 mRNA with or without polyadenylation
- Publication Part Number: 5994-0583EN
- Created: 18 Feb 2019
- 1 MB
High-throughput analysis for detection of CRISPR induced Homology Directed Repair (HDR) knock-in of novel restriction enzyme sites
- Publication Part Number: 5994-0524EN
- Created: 11 Feb 2019
- 675 KB
| Chinese (Simplified) (China) | Complete (PDF) |
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Visual sgRNA integrity quality assessment with separation of the linear and secondary structure fragments on the Agilent 5200 Fragment Analyzer system
- Publication Part Number: 5994-0523EN
- Created: 04 Feb 2019
- 1 MB
Agilent Automated Capillary Electrophoresis Systems General Safety Guide
- Publication Part Number: D0003433
- Created: 24 Sep 2024
- 2 MB
This application note introduces a method for target capture (long-read) sequencing using the Agilent SureSelect XT HS2 target enrichment system with some protocol modifications.
- Publication Part Number: 5994-7612EN
- Created: 21 Aug 2024
- 2 MB
The Agilent 5200 Fragment Analyzer system provides reliable sizing for fragments and smears for many nucleic acid applications
- Publication Part Number: 5994-0585EN
- Created: 19 Jan 2024
- 797 KB