Copy of microbial designs worksheet_03_08_091 by JimmyPavel

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									        Organism                Strain          Format           Application     Product number           General description                      Acession numbers
E.coli                   K12             4 x 44,000 feature    Universal       40010                                                   U00096
Salmonella typhimurium   SL1344          4 x 44,000 feature    Universal       40020
Salmonella typhimurium    LT2            4 x 44,000 feature    Universal       40021                                                   NC_003197
Mycobacterium            tuberculosis    4 x 44,000 feature    Universal       40030                                                   BUGS
Mycobacterium            4 strains       4 x 44,000 feature    Universal       40031                                                   BUGS
Streptomyces             coelicolor      4 x 44,000 feature    Universal       40040
Streptomyces             coelicolor      2 x 105,000 feature   Universal       40041
Neisseria species        NgFA1090        4 x 44,000 feature    Universal       40050                                                   BUGS
Neisseria species        NIST640         4 x 44,000 feature    Universal       40050                                                   BUGS
Neisseria species        053442          4 x 44,000 feature    Universal       40050                                                   BUGS
Neisseria species        FAM18           4 x 44,000 feature    Universal       40050              Universal designs can be used for    NC_008767
Neisseria species        MC58            4 x 44,000 feature    Universal       40050              comparative genomics, gene expressionNC_003112
Neisseria species        Z2491           4 x 44,000 feature    Universal       40050              studies and chromatin                BUGS
Staphylococcus aureus                    4 x 44,000 feature    Universal       40060              immunoprecipitation studies.         BUGS
Campylobacter jejunii    11168           8 x 15,000 feature    Universal       40070                                                   BUGS
Campylobacter jejunii    81116           8 x 15,000 feature    Universal       40070                                                   BUGS
Campylobacter jejunii    81176           8 x 15,000 feature    Universal       40070                                                   BUGS
Campylobacter jejunii    RM1221          8 x 15,000 feature    Universal       40070                                                   BUGS
Bacillus subtillis                       4 x 44,000 feature    Universal       40080                                                   NC_000964
Clostridium difficile    CD630           4 x 44,000 feature    Universal       40090                                                   BUGS
Clostridium difficile    qCD32g58        4 x 44,000 feature    Universal       40090                                                   BUGS
Clostridium difficile    CD196           4 x 44,000 feature    Universal       40090                                                   BUGS
Clostridium difficile    R20291          4 x 44,000 feature    Universal       40090                                                   BUGS
Cryptococcus gattii      gattii          1 x 244K feature      Universal       30110                                                   un-published (2007)
      Organism         Strain           Format           Application    Product number           General description                    Acession numbers




E.coli            K12             8 x 15,000 feature   Gene expression 030010                                                   U00096
E.coli            APEC 01         8 x 15,000 feature   Gene expression 030011            At least 1 probe per gene designed.    CP000468
E.coli            UPEC CFT703     8 x 15,000 feature   Gene expression 030012            Larger genes may contain several       AE014075
Cryptococcus      gattii          8 x 15,000 feature   Gene expression 30111             probes. Probe sets can be laid down in
                                                                                         duplicate or triplicate depending upon NC_008409, NC_005063,NC_007276,
                                                                                         genome size.                           NC_007277, NC_007278, NC_007279,
                                                                                                                                NC_007280, NC_007281, NC_007282,
T Brucei          TREU927         4 x 44,000 feature   Gene expression 030130                                                   NC_007283, NT_165288, NT_165287
E.coli            UPEC - CFT073   8 x 15,000 feature   Gene expression 030013
E.coli            Sakai:0157      8 x 15,000 feature   Gene expression 030014
E.coli            ETEC H1047      8 x 15,000 feature   Gene expression 030015
Pichea pastoris                   4 x 44,000 feature   Gene expression 030081                                               Integrated Genomics*
Pichea pastoris                   8 x 15,000 feature   Gene expression 030080                                               Integrated Genomics
       Organism                Strain          Format          Application     Product number           General description                         Acession numbers
E.coli                   K12            4 x 44,000 feature   ChIP-on-chip    010012                                                  U00096
Salmonella typhimurium   SL1344         4 x 44,000 feature   ChIP-on-chip    010021
Salmonella typhimurium    LT2           4 x 44,000 feature   ChIP-on-chip    010020
Mycobacterium            tuberculosis   4 x 44,000 feature   ChIP-on-chip    010031
E.coli                   0157 sakai     4 x 44,000 feature   ChIP-on-chip    010011             Tilling design with probes spaced       BA000007
E.coli                   APEC 01        4 x 44,000 feature   ChIP-on-chip    010014             reasonably evenly along the genome. CP000468
E.coli                   EPEC 2348      4 x 44,000 feature   ChIP-on-chip    010015                                                     NC_011601
                                                                                                On average 1 probe every 100bp,
E.coli                   UPEC CFT703    4 x 44,000 feature   ChIP-on-chip    010016                                                     AE014075
                                                                                                usually alternating between the forward
E.coli                   EAEC 042       4 x 44,000 feature   ChIP-on-chip    010017
                                                                                                and reverse strand.
E.coli                   ETEC H1047     4 x 44,000 feature   ChIP-on-chip    010018
E.coli                   W3110          4 x 44,000 feature   ChIP-on-chip    010019                                                  AP009048
E.coli                   EDL1933        4 x 44,000 feature   ChIP-on-chip    010001
Neisseria                FAM18          4 x 44,000 feature   ChIP-on-chip    010051                                                  NC_008767
Neisseria                MC58           4 x 44,000 feature   ChIP-on-chip    010052                                                  NC_003112
         Organism              Strain               Format          Application      Product number              General description                         Acession numbers
E.coli                   K12                 4 x 44,000 feature   aCGH             010012                                                     U00096
E.coli                   0157 sakai          4 x 44,000 feature   aCGH             020031                                                     BA000007
E.coli                   APEC 01             4 x 44,000 feature   aCGH             020032                   Tilling design with probes spaced CP000468
                                                                                                          reasonably evenly along the genome.
E.coli                   EPEC 2348           4 x 44,000 feature   aCGH             020033                                                        NC_011601
E.coli                   UPEC CFT703         4 x 44,000 feature   aCGH             020034                   On average 1 probe every 100bp, AE014075
E.coli                   EAEC 042            4 x 44,000 feature   aCGH             020035                usually alternating between the forward
E.coli                   ETEC H1047          4 x 44,000 feature   aCGH             020036                           and reverse strand.
E.coli                   W3110               4 x 44,000 feature   aCGH             020037                                                     AP009048
E.coli                   EDL1933             4 x 44,000 feature   aCGH             020038

* A license needs to be purchased from integrated genomics, for access to the Pichea pastoris genome sequence data.




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