source: trunk/uk/ac/ebi/Tab2MageImporter/tab2mage- genepix.txt @ 379

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1Experiment section 
2domain  ebi.ac.uk
3accession E-TOXM-XX
4quality_control "biological replicate (replicated hybridizations, marker redundancy on arrays) + positive/negative control (array quality)"
5experiment_design_type  compound_based_treatment
6name  Gene expression profiling in hepatocyte and neuron cell cultures following exposure to various chemical compounds
7description "22 chemicals on 2 cell lines, 2 concentrations and 2 exposure times, 2 replicates on custom arrays"
8release_date  15/05/2007
9submission_date 30/05/2007
10submitter Claude Reiss
11organization  "Vigilent Technologies, BioTeSys"
12publication title High throughput toxicogenomics
13authors "Reiss Claude, Reiss Christophe, Jürgen Bernardt, Ronald, Dirk Dressler"
14journal journal of toxicology
15volume  1
16issue 1
17pages 112-122                                                   
18year  2007                                                   
19
20
21
22Protocol section                                                     
23accession text  type  name  parameters                                             
24P-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                                             
25P-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                                               
26P-TOXM-3  blah  labeling  cDNA synthesis and labeling                                               
27P-TOXM-4  blah  hybridization Hybridization temperature(degree_C) ; duration(hr)                                             
28P-TOXM-5  blah  scanning  Scanning and Image analysis                                               
29
30Hybridization section                                                     
31File[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
32H_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
33H_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
34H_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
35H_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
36H_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
37H_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
38H_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
39H_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
40N_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
41N_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
42N_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
43N_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
44N_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
45N_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
46N_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
47N_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
48H_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
49H_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
50H_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
51H_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
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