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