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new data release - mouse genome project

Victoria Wang victoria at genome.wi.mit.edu
Thu May 8 17:28:09 EST 1997


hitehead Institute/MIT Center for Genome Research

Mouse Genomic Mapping Project

Data Release May 1997

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Genetic Map

The July 1996 Data Release was the final release of the Mouse Genetic
Map at
the Whitehead Institute/MIT Center for Genome Research. It reflects the
data
represented in the 14 March, 1996 issue of Nature. Please see this
paper,
and also Genetics 131:423-447 (1992) for descriptions of the materials
and
methods used to construct the maps.

Dietrich, W.F., J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles, Z.
Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T.J. O'Conner, C.A. Evans,
M.M.
DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A.
Jenkins, T.L. Hawkins, L. Stein, D.C. Page, & E.S. Lander (1996) A
comprehensive genetic map of the mouse genome. Nature 380:149-152.
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Mouse Physical Mapping Project

Having completed the genetic map, we are now constructing a physical map
of
the mouse consisting of 10,000 markers screened against a mouse YAC
library.
Many of the markers are the SSLPs that are also on the genetic map, but
are
also adding random STSs to the physical map to reach a total of 10,000
markers.

In this release, we include data for 7,796 markers successfully screened
against the YAC library. We have placed 6,361 of these markers into
singly-linked physical map contigs; 5,972 are in doubly-linked contigs.
All
the markers in doubly-linked contigs are linked to another marker in the
contig by at least two YACs, while markers can be joined to a
singly-linked
contig by only one YAC. Thus, the doubly-linked contigs are generally
smaller but more reliable.

The table below shows the number of physically and genetically-mapped
markers assigned to each chromosome. (Note that some markers that hit
yacs
have not yet been mapped to a particular chromosome, so the total number
of
physically-mapped markers in this table represents a subset of the total
number of markers in the release.) The right-most columns count the
number
of markers shared by the two maps ("BOTH"), and the total number of
distinct
markers mapped in any way ("TOTAL MARKERS").

Breakdown of Mapped Markers by Chromosome

 CHROMOSOME PHYSICAL  GENETIC  BOTH  TOTAL MARKERS
 Chr1       565       559      403   789
 Chr10      326       317      223   472
 Chr11      472       356      280   618
 Chr12      329       289      222   423
 Chr13      395       317      266   490
 Chr14      286       271      202   397
 Chr15      327       274      215   435
 Chr16      299       215      172   364
 Chr17      190       255      107   375
 Chr18      271       236      173   367
 Chr19      169       134      114   212
 Chr2       579       553      388   836
 Chr3       363       382      229   571
 Chr4       390       367      240   559
 Chr5       390       433      268   613
 Chr6       395       383      252   583
 Chr7       390       356      260   541
 Chr8       344       361      262   485
 Chr9       371       371      235   559
 ChrX       261       230      165   357
 TOTAL      7112      6659     4676  10046

YAC Library

The YAC library being used is described by Haldi, et al., in Mammalian
Genome 7:767-769 (1996). It consists of 40,000 YACs with an average
insert
size of 820 kb. The entire library, or individual YAC clones, is
available
through Research Genetics, Huntsville, Alabama (phone, 800-533-4363;
outside
US/Canada, 205-533-4363; FAX, 205-536-9016) and Genome Systems, Inc. of
St.
Louis, Missouri, (phone 800-430-0030). We are currently using a subset
of
24,000 clones in building the physical map. These 24,000 clones are
arrayed
here at the Center in a 5-dimensional pooling scheme. The STSs are
screened
on these 5D pools, with 3 hits describing a single YAC address, and up
to
two extra hits confirming that address.

STSs screened

Please note that this release of the physical map represents a work in
progress. It includes only those SSLPs that worked well on the first try
and
that did not require any special attention. There are now 5,112 SSLPs on
the
physical map, as well as 1671 random STSs and 882 genes and 130 others
(RFLPs, monomorphic markers, etc.). In future releases, we expect to add
primarily ESTs and random markers.

The genetically-mapped SSLPs are screened on the 5-dimensional pools,
using
the same pair of primers as were used when we placed them on the genetic
map. If the marker fails on the first try, it is run through the
screening
process a second time. If it fails twice, we attempt to convert the SSLP
into an STS by picking two new primers and an internal oligo from one
side
or the other side of the CA-repeat. Markers that fail this final step
will
probably not be placed on the physical map. If you are working with an
SSLP
that you want to know the precise placement of in relation to other
SSLPs
nearby, you may wish to consult the European Collaborative Interpecific
Mouse Backcross. They are mapping our SSLPs in a high-resolution
1000-animal
backcross. Chromosomes 2, 11, 15, 16, and 17 are completed, chromosomes
3
and 4 are nearly done, and others are underway.

Many of the markers on both the genetic and physical map are available
through Research Genetics, at a reduced cost under a community discount
arrangement set up by the WICGR. (Note: WI/MIT CGR has placed the
markers in
the public domain. The center and its personnel receive no financial
benefit
from the sale of primers.)

Citing this data

Data releases occur on a quarterly basis or more frequently if the
amount of
new data warrants it. At the end of each quarter, all genomic mapping
data
are reviewed and prepared for distribution via CGR's electronic
databases.
Data releases typically occur within two weeks of the close of the
month.
Releases are announced by electronic messages posted to the following
two
newsgroups: "bionet.genome.chromosomes" and "bionet.announce".

CGR's data release policy is among the most rapid, broad and regular of
any
genome center. Its purpose is to ensure that scientific colleagues have
immediate access to information that may assist them in the search for
genes. Data releases do not constitute scientific publication of CGR's
work,
but rather provide scientists with a regular look into our lab
notebooks.
For projects aimed at the analysis of particular genes or subchromosomal
regions, permission is hereby granted to use our data without the need
for a
formal collaboration, subject only to appropriate acknowledgment. For
projects aimed at large-scale mapping of entire chromosomes or entire
genomes, use of the data and markers should be on a collaborative basis.

References to this data in publications should be cited by listing each
of
the following three sources:

1. Dietrich, W.F., J. Miller, R. Steen, M.A. Merchant, D. Damron-Boles,
Z.
Husain, R. Dredge, M.J. Daly, K.A. Ingalls, T.J. O'Conner, C.A. Evans,
M.M.
DeAngelis, D.M. Levinson, L. Kruglyak, N. Goodman, N.G. Copeland, N.A.
Jenkins, T.L. Hawkins, L. Stein, D.C. Page, & E.S. Lander (1996) A
comprehensive genetic map of the mouse genome. Nature 380:149-152.

2. Dietrich, W.F. et al. (1994) A genetic map of the mouse with 4,006
simple
sequence length polymorphisms. Nature Genetics 7:220-245.

3. Copeland, N.G., D.J. Gilbert, N.A. Jenkins, J.H. Nadeau, J.T. Eppig,
L.J.
Maltais, J.C. Miller, W.F. Dietrich, R.G. Steen, S.E. Lincoln, A.
Weaver,
D.C. Joyce, M. Merchant, M. Wessel, H. Katz, L.D. Stein, M.P. Reeve,
M.J.
Daly, R.D. Dredge, A. Marquis, N. Goodman, E.S. Lander (1993) Genome
Maps
IV. Science 262:67.

4. Supplemented by additional markers in: Whitehead Institute/MIT Center
for
Genome Research, Genomic Map of the Mouse, Database Release 10, June
1996.

Additional publications with related information:

Dietrich, W., J. Miller, H. Katz, D. Joyce, R. Steen, S. Lincoln, M.
Daly,
M.P. Reeve, A. Weaver, P. Anagnostopoulos, N. Goodman, N. Dracopoli,
E.S.
Lander (1992) Genetic Maps. Stephen J. O'Brien, ed. Cold Spring Harbor
Laboratory Press.

Assay Conditions for the Genetic Map:

Assay conditions and other experimental details are given in:
Dietrich, W., et al., 1992. Genetics 131: 423-447.
Briefly, the PCR protocol used radiolabeled primers in a 25 cycle PCR (1
'94
degrees, 2' 55 degrees, 3' 72 degrees) on 20 ng of genomic DNA.

Contents of this Directory

 5-97.MarkerInfo.txt       PCR primer and product size
 5-97.GeneticMapInfo.txt   Genetic mapping information
 5-97.PhysicalMapInfo.txt  Physical mapping information
 5-97.STS2Contig.txt       Contig information (singly-linked)
 5-97.Contig2STS.txt       Contig information - inverted (singly-linked)
 5-97.STS2DoubleContig.txt Contig information (doubly-linked)
 5-97.DoubleContig2STS.txt Contig information - inverted (doubly-linked)
 5-97.Sequences.txt        Raw source sequences for STSs
 pictures/                 Maps in postscript and Macintosh format

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For further information contact: Victoria Wang
victoria at genome.wi.mit.edu or
Donna Slonim slonim at genome.wi.mit.edu

Last modified May 8, 1997



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