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
This archive was generated by hypermail 2b29 : Fri Jan 05 2001 - 08:42:46 EST