Changeset 451 for trunk


Ignore:
Timestamp:
Oct 30, 2007, 5:00:35 PM (15 years ago)
Author:
dominic
Message:

updated sample tab2mage files to remove problems with tab

Location:
trunk/uk/ac/ebi/Tab2MageImporter
Files:
3 edited

Legend:

Unmodified
Added
Removed

  • 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

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

    r379 r451  
    55accession E-BASE- E-BASE-1
    66quality_control   
    7 experiment_design_type  BiomolecularAnnotation 
    8 name  Experiment1 
    9 description test 
    10 release_date  00:00.0 
    11 submission_date 03/05/2007 
    12 submitter Root 
     7experiment_design_type  BiomolecularAnnotation
     8name  Experiment1
     9description test
     10release_date  00:00.0
     11submission_date 03/05/2007
     12submitter Root
    1313submitter_email   
    1414organization   
    1515publication_title   
    16 authors "PRS,DO" 
    17 journal EMBL journal     
    18 volume       
    19 issue      
    20 pages      
    21 year  2006     
    22 pubmed_id      
     16authors "PRS,DO"
     17journal EMBL journal
     18volume   
     19issue   
     20pages   
     21year  2006
     22pubmed_id   
    2323
    2424Protocol section       

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

    r450 r451  
    1919
    2020Protocol section
    21 accession text  type  name  parameters                  P-TOXM-1  "All chemicals tested were supplied by XXX" grow  Contaminant doses and mixture preparation medium;CO2;antibiotics
     21accession text  type  name  parameters
     22P-TOXM-1  "All chemicals tested were supplied by XXX" grow  Contaminant doses and mixture preparation medium;CO2;antibiotics
    2223P-TOXM-2  "RNA was isolated using a FastPrep instrument (Q-Biogene, Irvine USA) and Rneasy reagents (Qiagen)" extraction  RNA isolation and clean-up
    2324P-TOXM-3  text  labeling  cDNA synthesis and labeling
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