ABI 3730 DNA Analyzers

ABI 3730 PRISM® DNA Analyzers for:  
           - Sanger DNA sequence analysis
             - fragment length analysis

ABI3730

The ABI 3730 PRISM® DNA Analyzer enables high quality sequencing up to 1100 bases and high resolution (1 bp) fragment analysis. The ABI 3730 instruments is in the 96 or 384 well format using a 48 x 36cm capillary array.

For DNA sequencing we have the appropriate matrices set up on the instruments for BigDyeTM terminators v.3.1 and 1.1 (Applied Biosystems).

For fragment analysis the DNA can be labelled with up to four different fluorescent dyes. The fourth or fifth color, depending on the Dye Set used, is reserved for the internal lane size standard. We are using DS-33 (6-FAM; blue; VIC; green; NED; yellow; PET; red; LIZ, orange size standard).and DS-30 (6-FAM; blue; HEX; green; NED; yellow; ROX, red, size standard). We recommend the use of DS-33.

The core facility will provide start up theoretical and technical assistance for “hands-on” users. Each user reserves a date and time for occupying the instrument within iLab.

Order forms and price information within iLab

https://karolinska.corefacilities.org/service_center/show_external/3698/

Information regarding our “pre-made” and “full-service” options

Pre-made fragment analysis samples

Fragment analysis samples should be supplied to us as fluorescently labeled, pooled PCR products in 96-wells plates. The concentration of products needs to be optimized by the user.

Add the sample names in the column order (A01-H01, A02-H02 etc) in the order form.

An internal size standard, that allows precise size calling by providing a means to normalize mobility during the run, is added to each well. The users can bring their own internal standards or KIGene will supply the appropriate internal size standard. We stock 500 ROX, 500 LIZ and 600 LIZ. If another standard is needed it must be supplied by the user.

Each user must book an entire run (up to 48 samples).

Pre-made Sanger sequence samples

After completion of the sequence reaction, each sequence sample is precipitated and dried before delivery to us. We prefer to receive the samples placed in PCR plates or PCR strip-well tubes when sending more than 8 reactions.

Only mark the tubes with sample numbers and your initials. It is sufficient to write the complete sample names in the order form.

When sending plates: add the sample names in the column order (A01-H01, A02-H02 etc) in the order form.

Full-service Sanger sequence samples

In order to optimize the sequencing reaction we need information about template and primer concentrations, size of the template DNA and annealing temperature of the primer. Our requirements for template and primer concentrations can be found here:

KIGene sequencing service requirements and primers stocked at KIGene (pdf)

Our universal sequence primers

We stock the most common universal primers. Please note that the oligo sequences might differ between universal primers from different companies despite the same name. Remember to check that our universal primer can anneal to the target DNA. Our universal primers and their sequences are listed here:

KIGene sequencing service requirements and primers stocked at KIGene (pdf)

Sample delivery/ Drop box locations

The order form is submitted within iLab to the core and a hard copy is placed together with the samples in an envelope.

External Users 

Use padded envelope and parafilm over tube lids. For plates, rather use strip-well lids than plastic of foil covers to prevent evaporation. Place the plate on a tip rack or between two cardboard pieces to stabilize it and prevent lids snapping off during transfer.

Address:

KIGene, MMK, Translational Psychiatry, CMM L8:00, Karolinska University Hospital at Solna, 171 76 Stockholm.

Internal Users 

Send samples by internal mail or place samples in any of our four drop boxes at Solna Campus area. After 10:00, note that your samples might be processed faster if you place them in our CMM drop box.

CMM drop box

Pick-up time: 10:00 and 13:00 each business day
Drop box location: outside the Translational Psychiatry, L8:00 (CMM entrance floor)

BioClinicum drop box

Pick-up time: 10:00 each business day
Drop box location: Plan 5, close to the Skyway entrance

BioMedicum drop box

Pick-up time: 10:00 each business day
Drop box location: Plan 4, outside the lunchroom located close to the Skyway entrance

SciLifeLab drop box

Pick-up time: 10:00 each business day if iLab request is submitted before 9:30.
Drop box location: At the reception desk

Turn-around time

10:00 AM: sample-to-result within the same day
13:00 PM: pre-made sample-to-result within the same day

Note: In rare cases delays may occur if we experience unusually heavy loads or equipment failure.

Note: We always reload failed sequence reactions without charge in case we assess that they might improve in a second analysis.

Data and sample storage

We store all data from pre-made and full-service sequence samples for three years. Therefore, if you lose raw data files we can retrieve these for you if you provide the run date and sample names.

We save full-service template DNAs and primers for a month.

Sanger DNA sequencing information, our universal primers and troubleshooting

KIGene sequencing service requirements and universal primer list (pdf)

Sanger DNA sequencing FAQ and troubleshooting (pdf)