GC3F ACCESS DURING COVID-19 PANDEMIC
We are currently operating according to policies described in our approved Stage 1 Recovery Plan.
A summary of these policies is posted up around the core, as well as HERE.
FAQs ON GC3F's OPERATIONAL STATUS DURING COVID-19 PANDEMIC
CLICK HERE to get answers to our most frequently asked COVID-19 operational status questions.
NEW POLICY ON DATA RETENTION
We have had an increasing number of requests for the retrieval of old sequencing data from our archive. While we are always happy to help whenever we can, a couple of issues have arisen surrounding this. CLICK HERE to review our new policy on data retention & retrieval.
The GC3F offers nucleic acid fragment size analysis using an Advanced Analytical Fragment Analyzer.
To submit a samples for Fragment Analysis, please register for an iLab account and then click "Request Services" from the top menu bar in iLab. It is important that your request has been submitted in iLab before you provide the physical samples to us!
Please note: Fragment Analysis is included for all samples submitted for Illumina or PacBio sequencing (1 tube of sample per lane of sequencing). If you are submitting a single tube for sequencing and you are not in need of additional services, there is no need to request Fragment Analyzer service separately!
However, if you are submitting mutliple tubes for sequencing and wish for us to individually QC and multiplex them prior to sequencing, that is considered a separate Sample Prep request. Please contact email@example.com with questions.
The Fragment Analyzer is an automated capillary electrophoresis instrument that provides the same sort of data as an Agilent Bioanalyzer. It can resolve a broad range of DNA fragment sizes: Samples with fragment sizes between 1 and 6000 bp are characterized using NGS runs, or Small Fragment runs for higher resolution of small fragments under 1500bp. Larger genomic-sized DNA can be accurately sized on Large Fragment runs (up to 200 kb).
RNA samples can also be analyzed, and the instrument provides an “RNA Quality Number (RQN)” that is mathematically equivalent to the “RIN” values generated by Agilent Bioanalyzer instruments.
Pricing and Sample Submission
The Fragment Analyzer can run up to 11 DNA samples or 10 RNA samples (plus a control), with a ladder in the 12th well. For all analysis types, pricing is $50 per run even if you submit fewer than 10 or 11 samples, since all wells must be filled with reagents. If you have a small run and would like to save on cost, we suggest coordinating with another user prior to submission and we can then split the cost for you!
Please dilute your samples as indicated below and drop off a minimum of 3 µL of each sample in the labeled box in the GC3F freezer (located in 288 Klamath). Only 2 µL is used for the assay, but please provide at least 3 µL to account for pipetting loss.
|ANALYSIS TYPE||FRAGMENT SIZES IN RANGE||REQUIRED CONCENTRATION|
|NGS, cDNA, any other dsDNA||1 – 6,000 bp||0.1 – 10 ng/µL|
|Large Fragments (DNA)||75 – 200,000 bp||0.005 – 2 ng/µL|
|Small Fragments (DNA)||1 – 1,500 bp||0.2 – 5 ng/µL|
|RNA - High sensitivity||15 – 6,000 nt||0.1 – 10 ng/µL|
|RNA - Standard sensitivity||15 – 6,000 nt||5 – 500 ng/µL|
Fragment Anayzer capillary array