DSRG 2000 Study

Theodore Thannhauser tt34 at cornell.edu
Fri Jan 21 15:13:58 EST 2000


We are approaching the submission deadline for the DSRG 2000 study. If you
have requested and received materials to participate in this study please
send us your sequencing results and/or purified BAC template no later than
January 31, 2000. Note that the submission deadline for part 2 has been
extended to January 31. Information concerning the study and how to
participate can be found in an earlier message which is attached below:

 The purpose of this message is to remind you to participate in the DNA
 Sequencing Research Group's (DSRG) 2000 Study. In this two-part study we will
 focus on factors that affect the accuracy and quality of sequence when
 Bacterial Artificial Chromosomes (BACs) are used as the sequencing template.
 This study is being conducted with a view towards establishing official DSRG
 recommended methods. Since the large scale production of BACs is more
 problematic than that of standard plasmid templates we will not be able to
send
 the sample materials out in a mass mailing as we have done in the past (e.g.
 Standard and Difficult Template Studies). In order to participate in this
study
 it will be necessary to request materials in advance.
 
 Part 1 of the study will concentrate on the operational steps directly related
 to the sequencing of BACs. The DSRG will provide all registered participants
 with a sample of a standard BAC and an appropriate primer.  Participants will
 then sequence the standard BAC using the primer provided and the methods
 developed in their respective labs. We request that they send us the sample
 file electronically, in either .scf or .abi format, and a completed web form
 concerning the methodologies used to produce the sequence. The sequencing data
 will be analyzed and compared with the information available on the web form
 with a view towards identifying methods that correlate well with high quality
 sequence. Preliminary results will be presented at ABRF 2000.
 
 Part 2 of this study will concentrate on the operational steps relating to the
 isolation of BAC templates for use in sequencing. The DSRG will provide all
 registered participants with an agarose stab of bacteria containing the
 standard BAC. Participants will then grow up the bacteria and isolate the BAC
 by the methodologies utilized in their respective laboratories. We request
that
 they send the purified BAC to us for sequencing along with a completed web
form
 concerning the methods used in the isolation of this material. The sequencing
 results will be analyzed and compared with the information available on
the web
 form in order to identify practices that correlate well with high quality
 sequence. These will form the basis of the recommended method. Preliminary
 results will be presented at ABRF 2000.
 
 It is not be necessary to register for both parts in order to participate in
 this study, although we encourage everybody to do so. To request the materials
 necessary to participate in this study please use the following url:
 
 http://brcweb.bio.cornell.edu/dsrg2000/
 
 You will receive your sample of the standard BAC and/or the bacterial stab
 shortly after registering. Additional information concerning how to return the
 sequence, the purified BAC, where to find the web forms etc. will be provided
 at that time. 
 
 Please note: In conjunction with the 2000 Study we are also conducting a
 general survey of sequencing laboratories designed to give us an accurate
 picture of the composition and configuration of the average DNA sequencing
 laboratory. To take part in this survey please use the url given above.
 
 To be included in the preliminary presentation results, materials and surveys
 must be received by the following deadlines:
 
 Part 1: January 31, 2000
 
 Part 2: January 31, 2000
 
 General survey: January 31, 2000 
 
 I hope to hear from you all shortly! 
 
 Sincerely,
   
Theodore W. Thannhauser, Ph.D.
Director, BioResource Center
Rm. 149 Biotechnology Building
Cornell University
Ithaca, New York 14853-2703
Phone: (607) 254-4850
FAX:   (607) 254-4847
Email: tt34 at cornell.edu

http://brcweb.bio.cornell.edu
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