Ignore:
Timestamp:
Aug 22, 2007, 2:10:38 PM (15 years ago)
Author:
dominic
Message:

replaced to a public tab2mage genepix file

File:
1 edited

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  • trunk/uk/ac/ebi/Tab2MageImporter/tab2mage- genepix.txt

    r379 r406  
    44quality_control "biological replicate (replicated hybridizations, marker redundancy on arrays) + positive/negative control (array quality)"
    55experiment_design_type  compound_based_treatment
    6 name  Gene expression profiling in hepatocyte and neuron cell cultures following exposure to various chemical compounds
    7 description "22 chemicals on 2 cell lines, 2 concentrations and 2 exposure times, 2 replicates on custom arrays"
     6name  Gene expression profiling in cell cultures following exposure to various chemical compounds
     7description "2 cell lines, 2 concentrations and 2 exposure times, 2 replicates on custom arrays"
    88release_date  15/05/2007
    99submission_date 30/05/2007
    10 submitter Claude Reiss
    11 organization  "Vigilent Technologies, BioTeSys"
     10submitter john smith
     11organization  FETX
    1212publication title High throughput toxicogenomics
    13 authors "Reiss Claude, Reiss Christophe, Jürgen Bernardt, Ronald, Dirk Dressler"
     13authors "john smith"
    1414journal journal of toxicology
    1515volume  1
    1616issue 1
    1717pages 112-122                                                   
    18 year  2007                                                   
     18year  2005                                                   
    1919
    2020
     
    2222Protocol section                                                     
    2323accession text  type  name  parameters                                             
    24 P-TOXM-1  "All chemicals tested were supplied by Merck (Darmstadt, Germany) or Aldrich (Hannover, Germany). All were of highest purity grade" grow  Contaminant doses and mixture preparation medium;CO2;antibiotics                                             
    25 P-TOXM-2  "RNA was isolated using a FastPrep instrument (Q-Biogene, Irvine USA) and Rneasy reagents (Qiagen, Hilden Germany). RNA quality was checked with a 2100 Bioanalyser (Agilent Technologies, Palo Alto USA) by assessing the 28S/18S rRNA ratio." extraction  RNA isolation and clean-up                                               
    26 P-TOXM-3  blah  labeling  cDNA synthesis and labeling                                               
    27 P-TOXM-4  blah  hybridization Hybridization temperature(degree_C) ; duration(hr)                                             
    28 P-TOXM-5  blah  scanning  Scanning and Image analysis                                               
     24P-TOXM-1  "All chemicals tested were supplied by XXX" grow  Contaminant doses and mixture preparation medium;CO2;antibiotics                                             
     25P-TOXM-2  "RNA was isolated using a FastPrep instrument (Q-Biogene, Irvine USA) and Rneasy reagents (Qiagen)" extraction  RNA isolation and clean-up                                               
     26P-TOXM-3  text  labeling  cDNA synthesis and labeling                                               
     27P-TOXM-4  text  hybridization Hybridization temperature(degree_C) ; duration(hr)                                             
     28P-TOXM-5  text  scanning  Scanning and Image analysis                                               
    2929
    3030Hybridization section                                                     
    3131File[raw] Array[accession]  FactorValue[treatment]  FactorValue[compound] FactorValue[dose] FactorValue[exposure (hr)]  BioSource BioMaterialCharacteristics[Organism]  BioMaterialCharacteristics[OrganismPart]  BioMaterialCharacteristics[Cell type] BioMaterialCharacteristics[StrainOrLine]    Protocol[grow]  Parameter[medium] Parameter[CO2]  Parameter[antibiotics]  Extract Protocol[Extraction]  LabeledExtract  Protocol[Labeling]  Dye Hybridization Protocol[hybridization] Parameter[temperature(degree_C)]  Parameter[duration(hr)] Scan  Protocol[scanning]  Sample
    32 H_PropylParabenC1T1.gpr A-MEXP-XXXX   Propyl-paraben  IC50  24  bs1 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e1  P-TOXM-2  l1  P-TOXM-3  Cy5 h1  P-TOXM-4  40  40  scan1 P-TOXM-5  s1
    33 H_PropylParabenC1T1.gpr A-MEXP-XXXX   vehicle none  24  bs2 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e2  P-TOXM-2  l2  P-TOXM-3  Cy3 h1  P-TOXM-4  40  40  scan1 P-TOXM-5  s2
    34 H_PropylParabenC2T1.gpr A-MEXP-XXXX   Propyl-paraben  IC50/10 24  bs3 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e3  P-TOXM-2  l3  P-TOXM-3  Cy5 h2  P-TOXM-4  40  40  scan2 P-TOXM-5  s3
    35 H_PropylParabenC2T1.gpr A-MEXP-XXXX   vehicle none  24  bs4 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e4  P-TOXM-2  l4  P-TOXM-3  Cy3 h2  P-TOXM-4  40  40  scan2 P-TOXM-5  s4
    36 H_PropylParabenC1T2.gpr A-MEXP-XXXX   Propyl-paraben  IC50  48  bs5 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e5  P-TOXM-2  l5  P-TOXM-3  Cy5 h3  P-TOXM-4  40  40  scan3 P-TOXM-5  s5
    37 H_PropylParabenC1T2.gpr A-MEXP-XXXX   vehicle none  48  bs6 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e6  P-TOXM-2  l6  P-TOXM-3  Cy3 h3  P-TOXM-4  40  40  scan3 P-TOXM-5  s6
    38 H_PropylParabenC2T2.gpr A-MEXP-XXXX   Propyl-paraben  IC50/10 48  bs7 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e7  P-TOXM-2  l7  P-TOXM-3  Cy5 h4  P-TOXM-4  40  40  scan4 P-TOXM-5  s7
    39 H_PropylParabenC2T2.gpr A-MEXP-XXXX   vehicle none  48  bs8 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e8  P-TOXM-2  l8  P-TOXM-3  Cy3 h4  P-TOXM-4  40  40  scan4 P-TOXM-5  s8
    40 N_PropylParabenC1T1.gpr A-MEXP-XXXX Propyl-paraben ( IC50 for 24 hr ) exposed HepG2 cell culture supernatant  Propyl-paraben (IC50  IC50  24  bs9 Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e9  P-TOXM-2  l9  P-TOXM-3  Cy5 h5  P-TOXM-4  40  40  scan5 P-TOXM-5  s9
    41 N_PropylParabenC1T1.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  24  bs10  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e10 P-TOXM-2  l10 P-TOXM-3  Cy3 h5  P-TOXM-4  40  40  scan5 P-TOXM-5  s10
    42 N_PropylParabenC2T1.gpr A-MEXP-XXXX Propyl-paraben ( IC50/10 for 24 hr ) exposed HepG2 cell culture supernatant Propyl-paraben (CAS:94-13-3 IC50/10 24  bs11  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e11 P-TOXM-2  l11 P-TOXM-3  Cy5 h6  P-TOXM-4  40  40  scan6 P-TOXM-5  s11
    43 N_PropylParabenC2T1.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  24  bs12  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e12 P-TOXM-2  l12 P-TOXM-3  Cy3 h6  P-TOXM-4  40  40  scan6 P-TOXM-5  s12
    44 N_PropylParabenC1T2.gpr A-MEXP-XXXX Propyl-paraben ( IC50 for 48 hr ) exposed HepG2 cell culture supernatant  Propyl-paraben (CAS:94-13-3 IC50  48  bs13  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e13 P-TOXM-2  l13 P-TOXM-3  Cy5 h7  P-TOXM-4  40  40  scan7 P-TOXM-5  s13
    45 N_PropylParabenC1T2.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  48  bs14  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e14 P-TOXM-2  l14 P-TOXM-3  Cy3 h7  P-TOXM-4  40  40  scan7 P-TOXM-5  s14
    46 N_PropylParabenC2T2.gpr A-MEXP-XXXX Propyl-paraben ( IC50/10 for 48 hr ) exposed HepG2 cell culture supernatant Propyl-paraben (CAS:94-13-3 IC50/10 48  bs15  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e15 P-TOXM-2  l15 P-TOXM-3  Cy5 h8  P-TOXM-4  40  40  scan8 P-TOXM-5  s15
    47 N_PropylParabenC2T2.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  48  bs16  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e16 P-TOXM-2  l16 P-TOXM-3  Cy3 h8  P-TOXM-4  40  40  scan8 P-TOXM-5  s16
    48 H_PropylParabenC1T1-r.gpr A-MEXP-XXXX   Propyl-paraben  IC50  24  bs17  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e17 P-TOXM-2  l17 P-TOXM-3  Cy5 h9  P-TOXM-4  40  40  scan9 P-TOXM-5  s17
    49 H_PropylParabenC1T1-r.gpr A-MEXP-XXXX   vehicle none  24  bs18  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e18 P-TOXM-2  l18 P-TOXM-3  Cy3 h9  P-TOXM-4  40  40  scan9 P-TOXM-5  s18
    50 H_PropylParabenC2T1-r.gpr A-MEXP-XXXX   Propyl-paraben  IC50/10 24  bs19  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e19 P-TOXM-2  l19 P-TOXM-3  Cy5 h10 P-TOXM-4  40  40  scan10  P-TOXM-5  s19
    51 H_PropylParabenC2T1-r.gpr A-MEXP-XXXX   vehicle none  24  bs20  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e20 P-TOXM-2  l20 P-TOXM-3  Cy3 h10 P-TOXM-4  40  40  scan10  P-TOXM-5  s20
     32file1.gpr A-MEXP-XXXX   Propyl-paraben  IC50  24  bs1 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e1  P-TOXM-2  l1  P-TOXM-3  Cy5 h1  P-TOXM-4  40  40  scan1 P-TOXM-5  s1
     33file1.gpr A-MEXP-XXXX   vehicle none  24  bs2 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e2  P-TOXM-2  l2  P-TOXM-3  Cy3 h1  P-TOXM-4  40  40  scan1 P-TOXM-5  s2
     34file2.gpr A-MEXP-XXXX   Propyl-paraben  IC50/10 24  bs3 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e3  P-TOXM-2  l3  P-TOXM-3  Cy5 h2  P-TOXM-4  40  40  scan2 P-TOXM-5  s3
     35file2.gpr A-MEXP-XXXX   vehicle none  24  bs4 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e4  P-TOXM-2  l4  P-TOXM-3  Cy3 h2  P-TOXM-4  40  40  scan2 P-TOXM-5  s4
     36file3.gpr A-MEXP-XXXX   Propyl-paraben  IC50  48  bs5 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e5  P-TOXM-2  l5  P-TOXM-3  Cy5 h3  P-TOXM-4  40  40  scan3 P-TOXM-5  s5
     37file3.gpr A-MEXP-XXXX   vehicle none  48  bs6 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e6  P-TOXM-2  l6  P-TOXM-3  Cy3 h3  P-TOXM-4  40  40  scan3 P-TOXM-5  s6
     38file4.gpr A-MEXP-XXXX   Propyl-paraben  IC50/10 48  bs7 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e7  P-TOXM-2  l7  P-TOXM-3  Cy5 h4  P-TOXM-4  40  40  scan4 P-TOXM-5  s7
     39file4.gpr A-MEXP-XXXX   vehicle none  48  bs8 Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e8  P-TOXM-2  l8  P-TOXM-3  Cy3 h4  P-TOXM-4  40  40  scan4 P-TOXM-5  s8
     40file5.gpr A-MEXP-XXXX Propyl-paraben ( IC50 for 24 hr ) exposed HepG2 cell culture supernatant  Propyl-paraben (IC50  IC50  24  bs9 Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e9  P-TOXM-2  l9  P-TOXM-3  Cy5 h5  P-TOXM-4  40  40  scan5 P-TOXM-5  s9
     41file5.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  24  bs10  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e10 P-TOXM-2  l10 P-TOXM-3  Cy3 h5  P-TOXM-4  40  40  scan5 P-TOXM-5  s10
     42file6.gpr A-MEXP-XXXX Propyl-paraben ( IC50/10 for 24 hr ) exposed HepG2 cell culture supernatant Propyl-paraben (CAS:94-13-3 IC50/10 24  bs11  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e11 P-TOXM-2  l11 P-TOXM-3  Cy5 h6  P-TOXM-4  40  40  scan6 P-TOXM-5  s11
     43file6.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  24  bs12  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e12 P-TOXM-2  l12 P-TOXM-3  Cy3 h6  P-TOXM-4  40  40  scan6 P-TOXM-5  s12
     44file7.gpr A-MEXP-XXXX Propyl-paraben ( IC50 for 48 hr ) exposed HepG2 cell culture supernatant  Propyl-paraben (CAS:94-13-3 IC50  48  bs13  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e13 P-TOXM-2  l13 P-TOXM-3  Cy5 h7  P-TOXM-4  40  40  scan7 P-TOXM-5  s13
     45file7.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  48  bs14  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e14 P-TOXM-2  l14 P-TOXM-3  Cy3 h7  P-TOXM-4  40  40  scan7 P-TOXM-5  s14
     46file8.gpr A-MEXP-XXXX Propyl-paraben ( IC50/10 for 48 hr ) exposed HepG2 cell culture supernatant Propyl-paraben (CAS:94-13-3 IC50/10 48  bs15  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e15 P-TOXM-2  l15 P-TOXM-3  Cy5 h8  P-TOXM-4  40  40  scan8 P-TOXM-5  s15
     47file8.gpr A-MEXP-XXXX vehicle exposed HepG2 cell culture supernatant  vehicle none  48  bs16  Homo sapiens  Brain Neuron  SH-SY5Y   P-TOXM-1  RPMI  5%  penicillin  e16 P-TOXM-2  l16 P-TOXM-3  Cy3 h8  P-TOXM-4  40  40  scan8 P-TOXM-5  s16
     48file9.gpr A-MEXP-XXXX   Propyl-paraben  IC50  24  bs17  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e17 P-TOXM-2  l17 P-TOXM-3  Cy5 h9  P-TOXM-4  40  40  scan9 P-TOXM-5  s17
     49file9.gpr A-MEXP-XXXX   vehicle none  24  bs18  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e18 P-TOXM-2  l18 P-TOXM-3  Cy3 h9  P-TOXM-4  40  40  scan9 P-TOXM-5  s18
     50file10.gpr  A-MEXP-XXXX   Propyl-paraben  IC50/10 24  bs19  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e19 P-TOXM-2  l19 P-TOXM-3  Cy5 h10 P-TOXM-4  40  40  scan10  P-TOXM-5  s19
     51file10.gpr  A-MEXP-XXXX   vehicle none  24  bs20  Homo sapiens  Liver hepatocyte  HepG2   P-TOXM-1  DMEM  5%  penicillin  e20 P-TOXM-2  l20 P-TOXM-3  Cy3 h10 P-TOXM-4  40  40  scan10  P-TOXM-5  s20
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