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Project Documentation & Protocols: Maize Gene Discovery Project: Microarrays: Controls

Contents: Index | Progress | Controls | Libraries | Arrays | Data | Protocols | Ordering | Links | FAQs

Controls from several different sources will be used on the Maize Gene Discovery Microarrays. Sequences were either

  • contributed by members of this group and colleagues,
  • selected from our maize EST libraries because they have sequence homology to known 'house-keeping' or common genes or
  • acquired from a 'Plant Core Control Kit' being assembled by members of Dr. Pam Green's lab at Michigan State University (MSU).
  • Controls contributed by members of the Maize Gene Discovery Group include maize genes with known functions key to future experiments including MuDR genes, as well as transgenes, and contamination controls. 'Plant Core Control Kits' being developed at Michigan State University will likely be composed of genes from several different plant species. However, maize sequences have been contributed by the Maize Gene Discovery Project including several MuDR clones, Ac transposase, RuBISCO, ubiquitin, actin, EF1a, TUFA, PS1, HMG1, and Glutamine synthase. Some sequences from this kit have already been provided to us. Additionally we include several sequences of human DNA with low homology to maize genes as spiking controls.

    Contributed sequences were prepared by isolating plasmids from overnight bacterial cultures (alkaline lysis) and then sequenced for validation. PCR reactions were performed in multiple 75 ul reactions and analyzed by gel electrophoresis. PCR products were 'cleaned-up' using MultiScreen PCR Clean-up Plates (Millipore).

    If you need more information on any of the control genes, please contact the lab of origin.

    Plate Location Gene Name Plasmid Name Vector PCR Primers PCR Product Size Lab of Origin Arrays Printed On
    a1 Multi-drug resistance protein EST 11 MRP11 pSPOR1 "T7,T3" 0.7 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b1 Multi-drug resistance protein 40 5' UTR MRP40 pSPOR1 "T7,T3" 1.2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c1 Multi-drug resistance protein EST 15 MRP15 pSPOR1 "T7,T3" 1 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d1 Multi-drug resistance protein EST 23 MRP23 pSPOR1 "T7,T3" 0.95 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e1 Multi-drug resistance protein 29 3' UTR MRP29 pSPOR1 "T7,T3" 0.8 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f1 Multi-drug resistance protein EST 33 MRP33 pSPOR1 "T7,T3" 0.65 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g1 Multi-drug resistance protein EST 47 MRP47 pSPOR1 "T7,T3" 0.65 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h1 Multi-drug resistance protein EST 89 MRP89 pSPOR1 "T7,T3" 0.8 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a2 Multi-drug resistance protein EST 46 MRP46 pGM-T "T7,SP6" 1 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b2 Full length mudrB gene + TIR region PTIR/B pUC19 "M13F, M13R" 1.2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c2 Full length mudrB gene PB pUC19 "M13F, M13R" 0.73 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d2 MudR region 1-560 PTIR/A pUC19 "M13F, M13R" 0.57 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e2 MudrA cDNA (MuDR pos.450-1430) PAE1/2 pUC19 "M13F, M13R" 0.84 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f2 MudrA cDNA (MuDR pos.224-1430) PAUTR/E1/2 pUC19 "M13F, M13R" 0.95 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g2 MudrA cDNA (MuDR pos 1411- 2167) PAE2 pUC19 "M13F, M13R" 0.78 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h2 MudrA cDNA (MuDR pos. 2876-3140) PAE3 pUC19 "M13F, M13R" 0.28 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a3 (Gene MuDR) Mu* VC14 pBluescript SK+ "T7, T3" 1.1 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b3 (Gene MuRA) MuRA 3' Bam/EcoRI cDNA VC16 pBluescript SK+ "T7, T3" 0.47 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c3 (Gene MuRA) MuRA 3' Bam/HindIII cDNA VC17 pBluescript SK+ "T7, T3" 0.62 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d3 (Gene MuRA) MuRA HindIII 5' mid cDNA VC19 pBluescript SK+ "T7, T3" 0.8 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e3 3' EcoRI/PstI fragment of C1 cDNA C13'R/P pBluescript SK+ "T7, T3" 0.375 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f3 434 bp of a1 cDNA VC1 pBluescript SK+ "T7, T3" 0.43 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g3 a1 cDNA VC2 pBluescript SK+ "T7, T3" 1.3 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h3 a1 3' cDNA VC3 pBluescript SK+ "T7, T3" 0.45 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a4 610 bp of B1 cDNA VC11 pBluescript SK+ "T7, T3" 0.6 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b4 662 bp of c2 cDNA VC12 pBluescript SK+ "T7, T3" 0.65 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c4 435-1816 bp of C2 cDNA VC7 pBluescript SK+ "T7, T3" 0.45 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d4 a1 mid2-4c VC4 pBluescript SK+ "T7, T3" 0.4 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e4 MudrA VC15 pBluescript SK+ "T7, T3" 0.5 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f4 PL1 Jh7(p) VC10 pBluescript SK+ "T7, T3" 0.5 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g4 bronze1 (bz1 ex2 (5')) VC6 pBluescript SK+ "T7, T3" 0.35 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h4 KN1 cDNA ks3'Kpn pBluescript SK+ "T7, T3" 0.7 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a5 0.8kb KIN cDNA 87 EcoR1-XhoI pBluescript SK+ "T7, T3" 1 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b5 1.0 kb Knox1 gene cDNA pEV131 pBluescript SK+ "T7, T3" 1.2 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c5 1.0 kb Knox2 gene cDNA pEV4D pBluescript SK+ "T7, T3" 1.2 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d5 1.0 kb Knox 5 gene genomic b15-1 pBluescript SK+ "T7, T3" 1.2 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e5 0.8 kb Knox 6 gene cDNA EC2-3 pBluescript SK+ "T7, T3" 0.95 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f5 0.7 kb Knox7 gene cDNA EC2-4 pBluescript SK+ "T7, T3" 0.9 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g5 0.4 kb Knox 8 gene cDNA 17A1 pBluescript SK+ "T7, T3" 0.4 Hake lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h5 Maize GST1 cDNA PBS-GSTI pBluescript SK+ "T7, T3" 1.2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a6 Maize GSTIII cDNA PBSGSTIII pBluescript SK+ "T7, T3" 1.2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b6 Prolamine binding factor cDNA 300 bp AC#U82230 PBF pAD-Gal4-2.1 "605F, 605R" 0.5 Schmidt lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c6 1100 bp of B32 B32 pAD-Gal4-2.1 "605F, 605R" 1.2 Schmidt lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d6 420 bp of O2 O2 pAD-Gal4-2.1 "605F, 605R" 0.6 Schmidt lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e6 Elongation Factorr 1A 605077A07 pAD-Gal4-2.1 "605F, 605R" 1.3 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f6 Elongation Facrot 1A 605057B12 pAD-Gal4-2.1 "605F, 605R" 0.4 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g6 Elongation Facrot 1A 605017C01 pAD-Gal4-2.1 "605F, 605R" 1.6 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h6 Tubulin alpha 1/2/3 chain 605072H11 pAD-Gal4-2.1 "605F, 605R" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a7 Tubulin alpha 1/2 chain 605032H06 pAD-Gal4-2.1 "605F, 605R" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b7 Tubulin alpha 1/2 chain 605054G06 pAD-Gal4-2.1 "605F, 605R" 1.6 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c7 Tubulin alpha 3 chain 605028B02 pAD-Gal4-2.1 "605F, 605R" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d7 Arath act 1/7 actin 11 605053G09 pAD-Gal4-2.1 "605F, 605R" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e7 Actin 11 605017E10 pAD-Gal4-2.1 "605F, 605R" "1.5, 0.7" Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f7 Vacuolar ATPase 69 Kda subunit (A) 605077C08 pAD-Gal4-2.1 "605F, 605R" 1.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g7 Histone H1 homolog 605054D10 pAD-Gal4-2.1 "605F, 605R" 0.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h7 Histone H2A homolog 605058D08 pAD-Gal4-2.1 "605F, 605R" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a8 Histone H2A homolog 605065C09 pAD-Gal4-2.1 "605F, 605R" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b8 Histone H2A homolog 605088B07 pAD-Gal4-2.1 "605F, 605R" 0.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c8 Histone H4 605004D02 pAD-Gal4-2.1 "605F, 605R" 0.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d8 Rubisco subunit binding protein B subunit 606002C02 pBK-CMV "T7, T3" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e8 Rubisco subunit binding protein B subunit 605088A02 pAD-Gal4-2.1 "605F, 605R" "1.7,1" Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f8 Rubisco smaller subunit 707012E03 pGAD10 "707F,707R" 1.2 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g8 Rubisco smaller subunit 707050B11 pGAD10 "707F,707R" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h8 Rubisco larger subunit 687006H08 pBluescript SK- "T7, T3" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a9 Photosystem II 10 Kda polypeptide precursor 707001E07 pGAD10 "707F,707R" 0.9 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b9 Photosystem II 603025F08 pBluescript SK+ "T7, T3" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c9 Photosystem II 603006B05 pBluescript SK+ "T7, T3" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d9 Photosystem I 486072A01 pBluescript SK- "T7, T3" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e9 Photosystem I 687068B01 pBluescript SK- "T7, T3" 1.6 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f9 HMG1/2 like protein 606045H01 pBK-CMV "T7, T3" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g9 HMG1/2 like protein 606055D02 pBK-CMV "T7, T3" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h9 MNBB DNA binding protein 605070E11 pAD-Gal4-2.1 "605F, 605R" 1.1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a10 MNBB DNA binding protein 618049A09 pAD-Gal4-2.1 "605F, 605R" 0.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b10 Elongation factor TU 687044D07 pBluescript SK- "T7, T3" 1.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c10 Elongation factor TU 605019C05 pAD-Gal4-2.1 "605F, 605R" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d10 Elongation factor TU 605010F02 pAD-Gal4-2.1 "605F, 605R" 0.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e10 Elongation factor TU 605065A08 pAD-Gal4-2.1 "605F, 605R" 1.5 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f10 Glutamine synthase 603006F12 pBluescript SK+ "T7, T3" 1 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g10 Glutamine synthase 603029G03 pBluescript SK+ "T7, T3" 1.7 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h10 Ubiquitin 2 975bp VC18 pBluescript SK+ "T7, T3" 1.2 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a11 Ubiquitin 2 skubiquii cDNA VC9 pBluescript SK+ "T7, T3" 0.4 Chandler lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b11 BAR gene KS+BAR pBluescript SK+ "T7, T3" 0.8 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c11 BAR gene PGSABAR pBluescript SK+ "T7, T3" 1.5 Jorgenson lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d11 Luciferase gene PJD281 pUC18 "M13F, M13R" 2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e11 B-glucoronidase PJD327 pUC18 "M13F, M13R" 2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    f11 NPTIII KS+KMIII pBluescript SK+ "T7, T3" 1.2 Walbot lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    g11 "Human control, used as RT spikeing control" PHUM1 pT7T3 "T7, T3" 0.9 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    h11 "Human control, used as RT spikeing control" PHUM2 pT7T3 "T7, T3" 0.9 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    a12 "Human control, used as RT spikeing control" PHUM4 pT7T3 "T7, T3" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    b12 "Human control, used as RT spikeing control" PHUM5 pT7T3 "T7, T3" 0.8 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    c12 "Human control, used as RT spikeing control" PHUM6 pT7T3 "T7, T3" 0.6 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    d12 "Human control, used as RT spikeing control" PHUM7 pT7T3 "T7, T3" 0.4 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"
    e12 "Human control, used as RT spikeing control" PHUM8 pT7T3 "T7, T3" 0.6 Galbraith lab "605.03,605.04,605-05,606.01,614.01,614-02,486-01,UG1-1"

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