Welcome

International Triticeae EST Cooperative (ITEC)

Data Repository

If your group has sequence data to deposit for ITEC, please use the following steps to submit your data:
  1. Obtain an account for the Repository host machine for file-transfer-protocol (FTP) access either by (i) e-mailing Gerard Lazo (lazo@pw.usda.gov) or by (ii) filling out the first five lines of the form located at: http://wheat.pw.usda.gov/genome/cDNA.html. In your e-mail or on the form, identify your laboratory by the relevant person's name as designated in the list of ITEC participants (http://wheat.pw.usda.gov/genome/participants.html) and your choices for your account and password designations (fields Login ID and Login Password on the web form). Account names should be at least four characters long, beginning with a letter character (ie whelab). Passwords should contain alphanumeric characters and should be 5-15 characters in length. Also identify the Lab Code that your laboratory will be using (see next).

    Below is a table of currently established three-letter lab codes. Those that are highlighted are the same as used already in the "Catalogue of Gene Symbols for Wheat" (1998. Proc. 9th Intl. Wheat Genetics Symposium. McIntosh, Hart, Devos, Gale, & Rogers.). If your lab does not have a code established, you will need to submit a three-letter code (use lower case). To determine if a lab code has already been issued, please check the document "Reserved Laboratory Designators for DNA Clones, Primers and Markers (1999)". A description of how these codes are used in identifying loci may be seen in the document "Guidelines for Nomenclature of Biochemical/Molecular Loci in Wheat and Related Species; Revision of Section 5 and new Section 6". 

    Code#: Laboratory         : Other Codes                                
pwa  : Altenbach
whe  : Anderson
csb  : Appels             : cs, csa, csb, cshv, csih, csiha, csl, cssr
psr  : Bailey
abo  : Botha-Oberholster
tjc  : Close
scl  : Cloutier
ucw  : Dubcovsky
sfr  : Feuillet           : sfr, sfrp
unl  : Gill, B.           : ksu, unl
ksg  : Gill, K.
mcg  : Graner             : cmwg, mwg
scc  : Gustafson          : scc, scg, scs
hwm  : Herrmann/Wenzel
mhl  : Holdsworth
scu  : Holton
gbx  : Jacquemin
cnw  : Jia
mtd  : Joudrier           : mta, mtd
awb  : Langridge          : awb, bua, wua
jjl  : Lin
lkl  : Lapitan/Knudson    : lkl, bg
gcm  : Machray
ttu  : Nguyen             : ttp, ttr, tts, ttu, ttw
mug  : Ogihara
isc  : Pecchioni
slb  : Piffanelli
wws  : Schuch
tas  : Selvaraj
sun  : Shariflou
sun  : Sharp
wgc  : Sorrells           : bcd, cdo, cnl, og, rz, wg
wsu  : Walker-Simmons
mwl  : Warburton
                                                                      
# The listed Code is the directory name for the laboratory.
    You will receive confirmation by e-mail that your account has been established.

  2. Using your account, you should use an FTP application on your computer to transfer files for your laboratory to the Repository host machine at wheat.pw.usda.gov. (This will help limit account acccessibility only to ITEC members). Within your account, you may transfer your sequence and trace file data, or just the sequence data, to your designated directory. It is probably easiest to "tar" all your data into a single file and then do the file transfer. If helpful, you may also want to compress the file using "compress" or "gzip". Your login directory will be identified by the lab code selected for your group.

  3. If trace files are transferred, it is preferred that they be in SCF version 3 format. The program "makeSCF" will convert ABI/ALF files to the SCF format. The source code for makeSCF (ver 3.02, 03/98; Bonfield, Dear, & Staden) is located HERE or THERE.

  4. If you are able to trim off vector sequence, please submit the files in FASTA format. If you are not able to trim off vector, please also submit the vector sequence in FASTA format, and some information about the cloning procedures (enzymes used, linkers, etc...).

  5. For repository purposes, clones and DNA should be submitted in 96 well microtiter plates (Columns 1-12, Rows A-H). Preferred plates are Nunc Catalog No. 163320, but any standard microtiter plates are acceptable.

  6. Plates should be labelled by the 3-letter lab identifier (see above), a 3-digit consecutive number of the plates from each lab, and "c" or "d" (lower case) to indicate the plate contains cells or DNA:

    For example, whe is the lab code for Olin Anderson's laboratory - thus, the 13th plate pair from Olin's lab will be labelled WHE013d (for DNA) and WHE013c (for cells). Labelling the plates with upper case letters will help prevent mistaking things like "l" for "i", etc... Other EST projects have reported 15-20% error rates in keeping track of clones. It will be important to be careful/fussy about labelling and tracking.

  7. The designation of individual sequences will consist of the lab code, the plate number, a period, the position on the plate of the clone/DNA (i.e., column and row), whether it is a forward or reverse sequencing reaction (F or R), and the date (format YYMMDD) that the sequence was generated.

    For example, WHE013.D07F990405 is the sequence from the clone/DNA in position D07 on plate #013 from Olin Anderson's laboratory, sequenced on April 5, 1999 using forward primers.

  8. Shipping instructions are available: international shipping or domestic shipping.

    For questions:

    shipping and handling, contact:
           Phyllis Han (phyllish@pw.usda.gov, 510-559-5785).

    about computer set-ups and sequence handling, contact:
           Gerard Lazo (lazo@pw.usda.gov, 510-559-5640).

    other matters, contact:
           Olin Anderson (oandersn@pw.usda.gov)

  9. Eventually, we would like to have our cDNAs mapped. This is where having clones listed by lab and plate become important. Shown is a sample of how one sequence would evolve:

    1. Each laboratory is provided with a lab code (ie whe).
    2. Each microtiter dish contains 96-wells (Columns 1-12, Rows A-H).
    3. Each plate has a three-numeric positions in addition to the lab code (allowing for 1000 plates, 000-999).
    4. Thus the three-position lab-code and three-position numbering-code allows for 96,000 clones (WHE000c-WHE999c).
    5. Additional suffix information allows for multiple sequencing of the clones, differing by primer and date designations.
    6. For example, if we start with cDNA clone WHE013.D07 which comes from plate WHE013c.
    7. The DNA for the clone WHE013.D07 comes from plate WHE013d.
    8. Position WHE013.D07 should be equivalent for plates WHE013c and WHE013d, except that one plate is for the clone and the other is for DNA.
    9. The first sequencing of the DNA for clone WHE013.D07 is WHE013.D07F990405 (Note that the clone or DNA designator from the plate is not listed here).
    10. Repeat sequencing of this clone with same primers might look like WHE013.D07F990420 (same as above except for the date).
    11. If a different primer is also used on the same day for the clone, it might be WHE013.D07R990420 (same as above date, but different primer).
    12. A mapped locus with no biochemical identity might be Xwhe013.D07-1A (note primer code and date removed and character case change).
    13. If biochemical identity can be assigned to the sequence, perhaps the locus may evolve to Xwhe013.D07(Adh)-1A.
    14. Refer to the "Catalogue of Gene Symbols for Wheat" (1998. Proc. 9th Intl. Wheat Genetics Symposium. McIntosh, Hart, Devos, Gale, & Rogers.) for additional guides for locus definitions.

    Note: Numbering such as "001" and "002" are used in these instances to assist alignments and sorting of data by computer. This is currently in conflict with the "Catalogue of Gene Symbols for Wheat".