Ignore:
Timestamp:
Oct 30, 2007, 5:00:35 PM (14 years ago)
Author:
dominic
Message:

updated sample tab2mage files to remove problems with tab

File:
1 edited

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  • trunk/uk/ac/ebi/Tab2MageImporter/ta2mage- agilent.txt

    r379 r451  
    1515pages   337-342
    1616year  2006
    17 submission_date 15/06/2006                                                                   
    18 release_date  05/11/2006                                                                   
     17submission_date 15/06/2006
     18release_date  05/11/2006
    1919
    20 Protocol section                                                                     
    21 accession name  text  parameters  type                                                             
    22 P-NUTR-1  treatment   vehicle;route;preservation method; diet availability  grow                                                             
    23 P-NUTR-2  extraction  Total RNA was extracted with the Qiagen RNEasy Columns    extraction                                                             
    24 P-NUTR-3  labeling  Agilent low RNA Input Linear Amplification Kit using Cyanine-5-CTP    labeling                                                             
    25 P-NUTR-4  hybridization "17 hour incubation following Agilent protocols using 750ng of both Cy3 and Cy5 labeled material, In Situ Hybridization Kit reagents and control probes followed by a 10 minute room temperature wash in 6X SSC,0.005% tritonX-102 and 5 minutes at 4 degrees C in 0.1X SSC, 0.005% Triton X-102. The arrays were dried in a Nitrogen stream and scanned."  probe amount;duration hybridization                                                             
    26 P-NUTR-5  scanning  Arrays were scanned using an Agilent Scanner G2565AA .  scanner scanning                                                             
     20Protocol section
     21accession name  text  parameters  type
     22P-NUTR-1  treatment   vehicle;route;preservation method; diet availability  grow
     23P-NUTR-2  extraction  Total RNA was extracted with the Qiagen RNEasy Columns    extraction
     24P-NUTR-3  labeling  Agilent low RNA Input Linear Amplification Kit using Cyanine-5-CTP    labeling
     25P-NUTR-4  hybridization "17 hour incubation following Agilent protocols using 750ng of both Cy3 and Cy5 labeled material, In Situ Hybridization Kit reagents and control probes followed by a 10 minute room temperature wash in 6X SSC,0.005% tritonX-102 and 5 minutes at 4 degrees C in 0.1X SSC, 0.005% Triton X-102. The arrays were dried in a Nitrogen stream and scanned."  probe amount;duration hybridization
     26P-NUTR-5  scanning  Arrays were scanned using an Agilent Scanner G2565AA .  scanner scanning
    2727
    28 Hybridization section                                                                     
     28Hybridization section
    2929File[raw] Array[accession]  FactorValue[compound] FactorValue[Dose] FactorValue[Exposure(month)]  FactorValue[diet] BioSource BioMaterialCharacteristics[animal identifier] BioMaterialCharacteristics[Organism]  BioMaterialCharacteristics[StrainOrLine]  BioMaterialCharacteristics[Provider]  BioMaterialCharacteristics[Age] BioMaterialCharacteristics[DevelopmentStage]  BioMaterialCharacteristics[Sex] BioMaterialCharacteristics[OrganismPart]  Sample  Protocol[grow]  Parameter[diet availability]  Parameter[route]  Parameter[vehicle]  Parameter[preservation method]  SampleMaterial  Extract Protocol[extraction]  ExtractMaterial LabeledExtract  Protocol[labeling]  Dye LabeledExtractMaterial  Hybridization Protocol[hybridization] Parameter[duration] Parameter[probe amount] Scan  Protocol[scanning]  Parameter[scanner]
    3030GSM140954.txt Agilent-012694 Whole Mouse Genome G4122A      18  Standard Diet AIN-93G GSM140954 1 Mus musculus  C57BL/6 NIA 78 weeks  adult male  liver GSM140954 P-NUTR-1  ad libitum  oral    snap frozen in liquid nitrogen  whole_organ GSM140954 P-NUTR-2  total_RNA source1 P-NUTR-3  Cy3 cDNA  GSM140954   P-NUTR-4  17 h  750 ng  GSM140954   P-NUTR-5  Agilent Scanner G2565AA
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