From owner-celegans@net.bio.net Sun Apr 13 23:00:00 1997 Path: biosci!daresbury!not-for-mail From: Newsgroups: bionet.celegans Subject: 1997 C elegans Genetic Map Date: 14 Apr 1997 16:13:58 +0100 Lines: 359 Sender: lpddist@mserv1.dl.ac.uk Distribution: bionet Message-ID: <5ithjm$4tg@mserv1.dl.ac.uk> Original-To: celegans@dl.ac.uk -------------------------------------------------------------------- 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@mrc-lmb.cam.ac.uk Sylvia Martinelli cgc@mrc-lmb.cam.ac.uk Instructions on how to submit data ---------------------------------- Please send data to jah@mrc-lmb.cam.ac.uk or to cgc@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. --------------------------------------------------------------------- The forms (to be copied as many times as necessary) --------------------------------------------------- --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: ------------------------------------------------------------------ Notes ----- --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 ____________________________________________________________________ .