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CEPH Mega YAC clone

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Information

  • Clone : 35,712 clone
  • Vector : pYAC4 (EcoRI site)
  • Host strain : Saccharomyces cerevisiae AB1380.
  • Insert size : 560 kb (#613 to #731), 918 kb (#732 to #984).
  • DNA source : XY EBV human cell line.
  • Strage condition : AHC agar-stab.
  • References :
    • Chumakov, I. et al. Continuum of overlapping clones spanning the entire human chromosome 21q. Nature 359(6394): 380-387 (1992). doi: 10.1038/359380a0. PMID: 1406950.
    • Cohen, D. et al. A first-generation physical map of the human genome. Nature 366 (6456): 698-701 (1993). doi: 10.1038/366698a0. PMID: 8259213.
    • “The Genome Directory”, supplement to Nature 28 September 1995, vol. 377 issue no. 6547S.
    • Miller, P.L. et al. Internet-based support for bioscience research: a collaborative genome center for human chromosome 12. J. Am. Med. Inform. Assoc. 2 (6): 351-364 (1995). doi: 10.1136/jamia.1995.96157828. PMID: 8581551.
    • Wang, S.Y. et al. A high-resolution physical map of human chromosome 21p using yeast artificial chromosomes. Genome Res. 9 (11): 1059-1073 (1999). doi: 10.1101/gr.9.11.1059. PMID: 10568746.
    • Peterson, E.T. An integrated physical map for the short arm of human chromosome 5. Genome Res. 9 (12): 1250-1267 (1999). doi: 10.1101/gr.9.12.1250. PMID: 10613848.
  • Link
  • Please visit Informaion site for articles published by using this materials, references and tips.

Search for CEPH Mega YAC clone

Following process is maybe not best but how we find the particular YAC clone containing locus of interest by STS marker information.
Because end sequences of the YAC clone have not analyzed, the YAC clones are not mapped on a genome browser.
We show a case for human IGL locus (Gene ID: 3535, 22q11.2) as an example.

  1. set up your ftp client
    • ftp site information
      • ftp server: ftp.broadinstitute.org
      • user to access: anonymous
      • directory: /pub/human_STS_releases/july97/
  2. Download “07-97.YAC2STS.txt” data file to your computer. This file contains YAC clone ID with corresponding STS hits. Also download “README.html”.
  3. STS are positioned to the human genome available at the “UCSC Genome Browser”.
    Visit UCSC genome browser web site.
  4. Chose lates version of Human Assembly ex. “Human GRCh38/hg38”.
  5. Set region of chromosome and then click “go”.
  6. Set options as indicated below and click “refresh”.
  7. STS markers will show up on top panel.
  8. Click STS name. Click the right button of your mouse to “Open details page in new window…”.
  9. STS maker info will show up.
  10. Please find “STS Marker, Start, End and Other names”.
  11. Copy these items to a table of Excel file.
  12. Find the STS marker and corresponding YAC in the “07-97.YAC2STS.txt”.
    I hope you or your colleague can handle MS-DOS command. The following text is an example of a batch file.

        set target=”07-97.YAC2STS.txt”
        echo “RH48655” >result.txt
        find /I “RH48655” %target% >>result.txt
        echo “STSG30889” >>result.txt
        find /I “STSG30889” %target% >>result.txt
        echo “WI-362” >>result.txt
        find /I “WI-362” %target% >>result.txt
        echo “D22S636” >>result.txt
        find /I “D22S636” %target% >>result.txt
        echo “AC22-362” >>result.txt
        find /I “AC22-362” %target% >>result.txt
        echo “PH838” >>result.txt
        find /I “PH838” %target% >>result.txt
        :
  13. Put YAC ID to the Excel.
  14. The clone you find now maybe include false-positive. So please find the clone which hit multiple STS of locus. With this way, you may find the clone usable for your research at last.

(GRP0063e 2004.02.13 T.M.)

2022.12.10



 

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