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1997 GENETIC MAP OF C. ELEGANS -- CALL FOR GENETIC MAP DATA
The deadline for submitting data for inclusion in the
1997 Genetic Map of C. elegans is
*** 30 APRIL 1997 ***
This is a general call for data on new and old genes,
polymorphisms, rearrangements and other genetic information,
pertaining to the nematode Caenorhabditis elegans. As well as
periodic updates of ACeDB, a full revision and updating of the
C. elegans Genetic Map is carried out every two years, and a printed
version of the map is published and distributed as an issue of The
Worm Breeder's Gazette. This work is carried out as a subcontract for
the Caenorhabditis Genetics Center (see WBG 14(5): 11 - 13).
The rest of this message contains updated instructions for
submitting data by e-mail. We are still very happy to receive data by
regular mail (though submission by e-mail does make less work for us).
We are also very happy to receive comments, corrections and
suggestions for improvement.
All genes, alleles, polymorphisms and strains should have
standard CGC names. For a summary of recommended genetic nomenclature
for C. elegans, see the Genetics section of the Caenorhabditis elegans
WWW Server at UTSW (also Horvitz et al (1979) Mol Gen Genet
175:129-133, and WBG (1987) Vol 10 No 1 pp 1-5). For new genes,
polymorphisms and rearrangements, which have not already been notified
to Jonathan Hodgkin (CGC map curator), we would appreciate a "--Gene"
or "--Polymorphism" or "--Rearrangement" entry. This is particularly
important for polymorphisms, since they are only really useful when
they have physical map locations.
Jonathan Hodgkin jah at mrc-lmb.cam.ac.uk
Sylvia Martinelli cgc at mrc-lmb.cam.ac.uk
Instructions on how to submit data
----------------------------------
Please send data to
jah at mrc-lmb.cam.ac.uk
or to
cgc at mrc-lmb.cam.ac.uk
which is a joint account, created for this purpose.
Receipt of all data submitted by e-mail will be acknowledged. If you
do not receive an acknowledgement within 7 days, please send the data
again.
You can submit many separate pieces of data in a single e-mail letter.
The letter can also start with a normal letter, e.g. describing what
follows, before the data begin. Please start each piece of data with
the appropriate header line that begins with "--", leave a blank line
between each separate data entry, and do not leave any blank lines
within an entry. The fields starting with a "*" are optional. The
fields with a "+" can be repeated. Please follow the style of the
examples as closely as possible.
Although we are providing forms to ease transcription into a standard
form, all the data will be reviewed by hand to check for consistency.
In particular, if there is any ambiguity or relevant extra
information, add it as a comment.
Please give full genotypes including allele names for all crosses.
When using polymorphisms in mapping data, give them as a gene in the
genotype (as shown in the example). When giving molecular data on
deficiencies, use the Df/Dp data form and give the name of the
probe (or PCR pair) in the Gene field. Please also tell us what this
name stands for, and what cosmids/YACs it maps to, in a comment.
When giving positive or negative clones for a gene or polymorphism,
please indicate in parentheses how this was established, e.g. by
transformation rescue etc. (see examples).
Formatting guidelines (also see examples):
When there are several items on a line, such as several alleles,
use commas to separate them.
Do not put a full stop or semicolon at the end of lines, except for
Comment or Description lines.
When giving names of people (e.g. the mapper for map data) give the
surname followed by all initials, without spaces or full stops between
initials.
Give dates just as month/year.
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The forms (to be copied as many times as necessary)
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--Gene
Gene_name:
Data_provider:
*Allele:
*Positive_clone:
*Negative_clone:
*Complementation_data:
*Description:
*+Comment:
--Polymorphism:
Polymorphism_name:
Data_provider:
*Origin:
Detection_method:
Positive_clone:
*Negative_clone:
*+Comment:
--Rearrangement
Rearrangement_name:
Data_provider:
Genes_included:
*+Comment:
--Breakpoint
Rearrangement:
Data_provider:
Positive_clone:
*Negative_clone:
*+Comment:
--2 point data
Mapper:
Date:
Temp:
Genotype:
*Mapped_genes:
Results:
Calculation:
*+Comment:
--Df/Dp data
Mapper:
Date:
Genotype:
*Rearrangement:
*Gene:
Results:
*+Comment:
--Multi-point data
Mapper:
Date:
Genotype:
GeneA:
GeneB:
*A_non_B_results:
*B_non_A_results:
*Combined_results:
*+Comment:
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Notes
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--Rearrangement
Use this entry only for reporting new rearrangements and balancers;
otherwise, use --Breakpoint and --Df/Dp data entries.
--2 point data
You need only give the names of the mapped genes if more than two
genes are mentioned in the genotype.
The calculation line is designed to help us combine data correctly.
It replicates some information from the Results line together with an
initial keyword describing how the map distance calculation should be
performed. After the keyword should follow the numbers to be used in
the calculation, by themselves without phenotypes. Three commonly
used types are given below, and a more extensive listing is also
available. In some cases the same calculation keyword may be
appropriate even when a cross is done slightly differently, e.g. when
using a dominant gene in cis to a recessive one. Almost all 2 point
data reported for C. elegans thus far can be classified into a total
of 19 different types. A description of these 19 types, together with
specific examples from the existing database, will be supplied by e-mail
if desired.
Calculation Data used How calc is done
----------- --------- ----------------
Full WT X Y XY (2p-p^2)/2 = (X+Y)/(WT+X+Y+XY)
One_recombinant WT X (2p-p^2)/3 = X/(X+WT)
Selected X XY (2p-p^2) = X/(X+XY)
Note that this is a guide for us on how to do the calculation; you do
not need to submit a calculated distance.
--Df/Dp data
Again, give the names of the rearrangement (Df or Dp) or gene only if
there is a complex genotype.
The Results line should contain one of the following:
xDfA deletes geneB
xDfA does not delete geneB
xDpA includes geneB
xDpA does not include geneB
xDpA includes xDfB
xDpA does not include xDfB
xDfA overlaps xDfB
xDfA does not overlap xDfB
--Multi-point data
This is designed to capture 4 point, 5 point, n-point experiments as
well as 3 point. The presumption is that you are selecting for
recombinants between GeneA and GeneB, and measure how many carry each
additional marker. Give all markers in the genotype, and specify
which markers were selected for, using the GeneA and GeneB fields.
There are three possible results lines, one for A_non_B recombinants
one for B_non_A recombinants, and one for combined results. We
encourage you to give non-combined results if possible.
On the results lines we would like alternating genes and numbers,
starting with geneA and ending with geneB. If there are no
recombinants between two genes, then give 0. Note that even if there
are no recombinants between e.g. geneA and geneC, and you believe that
geneC maps outside geneA, we request you keep geneA at the left end of
the results line. e.g.
geneA 7 geneC 3 geneB ! well-defined order
geneA 0 geneC 15 geneB ! geneC probably left of geneA
geneA 15 geneC 0 geneB ! geneC probably right of geneB
Examples
--------
(the comments after "!" are not part of the message)
--Gene
Name: yog-1
Data_provider: Other AN
Allele: e3000, e3001
Positive_clone: C52D6 (stable transformation rescue)
Negative_clone: ZK354 (failure to rescue)
Description: yog for yoga. adult worms tie themselves into reef-knots,
L1's into granny knots. Lives 6 months. Does not mate.
Complementation_data: complements unc-151(e3456), age-22(n9999)
--Gene
Name: obr-1
Data_provider: Other AN
Positive_clone: Y17D6, Y21H3 (hybridisation to Yac polytene filter)
Description: related to human obesity-determining gene OB by sequence
similarity.
--Polymorphism
Name: eP2000
Data_provider: Other AN
Origin: Tc1 in high hopper strain
Detection_method: lambda2612 probing EcoRI southern
Positive_clone: C16D12 (fingerprint of lambda2612)
--Rearrangement
Rearrangement_name: eDf100
Data_provider: Other AN
Genes_included: dpy-13, yog-1
Comment: U235 induced.
--Breakpoint
Rearrangment: eDf100
Data_provider: Other AN
Positive_clone: T16C12 (EcoRI, HindIII polymorphisms)
--2 point data
Mapper: Brenner S ! surname initials
Date: 01/72 ! just month and year
Temp: 20
Genotype: sma-4(e729) unc-32(e189)/+ +
Results: 928 WT, 9 Dpy, 8 Unc, 326 DpyUnc
Calculation: Full 928 9 8 326
--2 point data
Mapper: Brenner S
Date: 4/70
Temp: 20
Genotype: sma-2(e297) unc-36(e251) / + +
Results: 482 WT, 2 Unc, 1 Sma, 117 SmaUnc ! numbers with phenotypes
Calculation: One_recombinant 482 2 ! see explanation above
Comment: used One_recombinant not Full because
of deviation from Mendelian ratios ! any text you want
--Df/Dp data
Mapper: Hodgkin JA
Date: 9/78
Genotype: eDf1(e1405)/her-1(e1518) unc-42(e270) sma-1(e30) XO
Gene: her-1
Results: eDf1 does not delete her-1 ! see above for allowed list
--Df/Dp data
Mapper: Other AN
Date: 1/94
Rearrangement: eDf100
Gene: cm12c12
Results: eDf100 deletes cm04g11
Comment: cm04g11 is a cDNA hybridising to Y38B9 and Y4C6
on the polytene grid, assayed by PCR.
! actually for cDNAs that the sequencing consortium has mapped
! you do not need to give the positive clones.
--Multi-point data
Mapper: Hodgkin JA
Date: 1/82
Genotype: her-1(e224)/dpy-11(e1518) unc-42(e270)
GeneA: dpy-11
GeneB: unc-42
A_non_B_results: dpy-11 27 her-1 0 unc-42
B_non_A_results: dpy-11 31 her-1 2 unc-42
--Multi-point data
Mapper: Hodgkin JA
Date: 05/83
Genotype: mor-2(e1125)/unc-5(e53) him-8(e1489) dpy-20(e1282)
GeneA: unc-5
GeneB: dpy-20
Combined_results: unc-5 1 mor-2 7 him-8 2 dpy-20
--Multi-point data
Mapper: Other AN
Date: 12/97
Genotype: unc-5(e53) dpy-20(e1282)/eP2000 eP2001 eP2002 eP2003
GeneA: unc-5
GeneB: dpy-20
A_non_B_results: unc-5 0 eP2000 13 eP2003 0 eP2001 6 eP2002 1 dpy-20
Comment: polymorphism data
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