Technology Overview
The Agilent Fragment Analyzer system is a nucleic acid analysis tool that can analyze a wide range of samples, including cDNA, NGS libraries, PCR fragments, and total RNA etc. Having high-throughput in a single operation, the Agilent Fragment Analyzer accelerates the nucleic acid analysis in molecular workflow.
The system is a reliable and cost-effective alternative to the Bioanalyzer 2100, providing comparable and robust results. It features improved sensitivities and resolution in detection. Its analysis software provides accurate and detailed results on sample size distribution and quality for downstream processes and various workflows, including QC for NGS library, Single Cell (10X) cDNA and library, and routine RNA integrity assessment.
While the assays provide precise information on the size distributions of fragments, it is not recommended for accurate quantification of sample concentration. For precise measurements of DNA or RNA concentration, fluorescent dye methods such as Qubit or PicoGreen assay are suggested.
Workflow
Sample Preparation and Submission
Sample Preparation and Submission Guidelines
(1) Prepare samples according to the sensitivity range provided in the table below and submit them in the designated vessel types stated below. Please label the tubes/strips/plates clearly and provide the full names of the sample in the sample submission form.
| Sample Quantity | Vessel Type | Remarks |
| ≤ 8 | 1.5 mL tubes | |
| 9 – 32 | 8-well strips with caps | |
| > 32 | 96-well plate | 1. Arrange samples by column, i.e. fill down A1 – H1 -> A2 – H2 and so on. |
| 2. For DNF-474 users (DNA samples), leave well H12 empty for ladder. | ||
| 3. For DNF-472 users (RNA samples), leave last column (A12 – H12) empty for ladder. |
(2) Based on our in-house experience, it is advisable to aim for a concentration around the midpoint of the sensitivity range, as this tends to yield the best results. Concentrations towards the lower end of the range may not provide reliable data.
| Fragment Analyzer Assay | Sizing Range | Recommended Concentration Range | Minimum Sample Volume | Maximum number of samples per plate |
| DNF-474 HS NGS Fragment Kit (1 – 6,000 bp) | 100 – 6,000 bp | Sharp Peak*: 0.25 – 0.5 ng/μL | 5 μL | 95 |
| Broad Peak**: 1.25 – 2.5 ng/μL | ||||
| DNF-472 HS RNA Kit (15 nt) | 200 – 6,000 nt | Total RNA: 2.5 – 5 ng/μL | 5 μL | 88 |
*e.g. amplicon
**e.g. NGS library
(3) Clearly label each tube with sample ID. If strips are being used, label the sample tubes with number corresponding to sample name on the sample submission form.
If plate(s) are being used, record plate ID on BOTH the submission form and the plate(s).
(4) Submit service request through iLab. Unless otherwise specified, a smear analysis between 200 bp and 1,000 bp would be included in the report for all DNA assays.
(5) Submit completed Fragment Analyzer sample submission form as attachment on iLab.
(6) Contact platform specialist for sample submission appointment.
(7) Bring the samples to the Fragment Analyzer Platform at the Core.
Special notes for Illumina Sequencing (Next Generation Sequencing) users
Please contact our Illumina platform specialists (nextgenseq.cpos@hku.hk) prior to submitting your samples to the Core.
*IMPORTANT*: It is not recommended to rely on the concentration indicated on the Fragment Analyzer report for NGS library quantity check and NGS sequencing preparation. We advise using qPCR for accurate measurement of NGS library concentration.
For more details about submission requirements for Illumina Sequencing, kindly visit the Illumina Sequencing Sample Requirements and Submission webpage.
If your samples do not meet above requirements, please feel free to reach out to us (fragmentanalyzer.cpos@hku.hk / 2831-5479) for assistance.
Data Collection
Processing Time
The expected turnaround time is usually 1 – 3 working days.
Data Delivery
Results will be delivered in PDF format via our Online Data Delivery System (ODDS).
Unless otherwise specified, a smear analysis between 200 bp and 1,000 bp would be included in the report for all DNA assays.
Terms of Service
Leftover Samples
Leftover samples will be kept for one week after the delivery of results.
Users are welcome to collect any leftover samples during this period, after which the samples will be discarded without further notice.
Please contact our platform specialist for sample pick-up arrangement.
Contact
Mr Jacky CHAN
