Hi Jennifer,
At the lab, we have sequencher. We are able to view the data.
There are many options to save the data files from MJ's Basestation.
However, ABI format is not one of them.
I think DNA sequencing community is so use to using ABI file type that we
all tend to ignore the other file types that are excepted by other DNA
sequencing editors/programs.
I'm sure that any editor will be able to open the files as long as the file
type is accepted by the down stream program.
-- Jeremy Medalle Lab Coordinator The Rockefeller University 1240 York Ave Box 105 NY, NY 10021http://www.protein13-pc.rockefeller.edu
> From: "Jennifer Brosius" <jbrosius@valigen.net> > Reply-To: <jbrosius@valigen.net> > Date: Mon, 11 Dec 2000 13:38:51 -0500 > To: "'Jeremy Medalle'" <medallj@mail.rockefeller.edu>, "Recipients of ABRF > List" <abrf@aecom.yu.edu> > Subject: RE: MJ research DNA Sequencer(Basestation) > > Hi Jeremy, > > You mentioned the data files are not in ABI format. What > type of format are the data files? Did you happen to use the > data in any type of "downstream" analysis? Were you able to > import the data into some type of sequence analysis software? > Not to be "firing" questions at you, but any type of "outside" > user info/feedback is very appreciated. Thank you in advance. > > > Jennifer Brosius > Sequencing Technologist > ValiGen > 300 Pheasant Run > Newtown, PA 18940 > Phone:(215)504-4444 > Fax:(215)504-1546 > http://www.Valigen.net > > > > > -----Original Message----- > From: Jeremy Medalle [mailto:medallj@mail.rockefeller.edu] > Sent: Friday, December 08, 2000 11:58 AM > To: Recipients of ABRF List > Subject: MJ research DNA Sequencer(Basestation) > > > Attention DNA Sequencers: > > I work at The Rockefeller University in DNA Sequencing Lab of Protein/DNA > Technology Center. We sequence over 90, 000 samples a year. Please note > that I am not a MJ research representative/sale. > > I would like to hear from other people who are using the Basestation from MJ > research or submitted samples/saw their DEMO for this machine(Basestation). > > This machine use slab technology with the ability to run 96 samples from any > chemistry. > > Yesterday, I attended their demo by Christopher Abbott, Product Support > Specialist. I was able to run my own 96 samples (BigDye terminator) from > start to finish on the Basestation(11am-4pm). > > The Basestation seems to good to be true for a 96-high-throughput machine. > The software, i.e. Cartographer Analysis, seems user-friendly and screen > size fits in one panel to view gel image, electropherogram data, and list of > sample runs. > > Below are my PROS and CONS for the machine/software. > > PROS > > *** No matrix to run. However you can make your own if your not satisfied. > *** Changing chemistries(i.e. big dye terminators to primer to other > chemistry) are easy with a change of a mirror in the Base station. > If the wrong module is selected in the computer, it can still be > changed. > *** 1 ul out 20-35 ul of sample(in formamide) is loaded from our 1:1 > Big Dye reactions. > *** Loading trays can be taking out before the runs starts for repeats > or a second, third, ..., or twenty sequencing verification. > *** Gel washing for machine setup is nonexistent. (Laser passed through > the top glass and the excitation is pick up on the same side.) > *** Glass plates are smaller and compact. > *** Gel polymerization takes 5 minutes under UV light with a > photoinitiator. No APS, No temed, and No RUSH. > *** Upper/lower buffer chambers are attached to top plate, i.e. no > buffer leaks and less buffer used. > *** Cooling plate is on the platform. > *** Gel loading of 96 samples is automated(takes about ~25 minute till > the run starts). > *** Software is easy to learn. Scroll down cheat sheet included. > *** Software license allows for up to 10 computers in the lab. > *** Phred scores can be given to each sequence and scores are exportable > to Excel documents. > *** Tracking 96 lanes are fast(1-2 minutes). You can retract by one > lane automatically! You can use your mouse to draw the tracking lane! > *** Graphics after gel extraction are great. > *** Electropherogram data can be manipulated to give even peak heights > using different modules. They actually make a big difference in > the appearance and electropherogram data is changed. Therefore, > the user see the same appearance. > > > CONS > > *** Data files are not in ABI format(Later version will have this > option). > *** Gel display before tracking is only one expanded view. > It is not a good representation of the data. > *** Trim is all 96 samples and not individually. > *** Staggered loading is not a option but can be done by loading > even sample first(w/ even sample sheet) and then restarting the > run to load the odd(w/ odd sample sheet). In the end, the correct > sample sheet is re-installed. > > Notes: > > *** There is an external heating/cooling system. I.e. water bath at 40'c. > *** Maintenance looks low. A H2O bottle and a tray of 10X are the > only thing to clean after the run. > *** Its seems that there is no text files produced. Files format > can be used with any editor. > *** It runs on a PC. It ahs a CD burner. > > > Kudos to MJ Research, Guoshan Tsen, and Christopher Abbot. > > > -- > Jeremy Medalle > Lab Coordinator > The Rockefeller University > 1240 York Ave > Box 105 > NY, NY 10021 > > http://www.protein13-pc.rockefeller.edu > > >
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