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E-CAGE-155.idf

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					            Transcription profiling of Arabidopsis cotyledons infected with Hyaloperonospora parasitica for different time periods
Investigation Title
            CAGE_HRI_cotyledon_pathogen
Comment[Submitted Name]
            development_or_differentiation_design
Experimental Design replicate_design            individual_genetic_characteristics_design by array
                                                            reference_design
                                     organism_part_comparison_design   transcription profiling
            mo:1.3.1.1 mo
Experimental Design Term Sourcemo     REF                   mo         EFO
            2006-10-31
Comment[ArrayExpressReleaseDate]
            4
Comment[AEMIAMESCORE]
            E-CAGE-155
Comment[ArrayExpressAccession]
            2010-07-29 16:39:59 Last Changed Rev: 13058
Comment[MAGETAB TimeStamp_Version]
            period of infection
Experimental Factor Namepathogen
            time
Experimental Factor Typeinfect
Experimental Factor Term Source REF
            Zhang
Person Last Name
            Cunjin
Person First Name
Person Mid Initials
Person Emailcunjin.zhang@warwick.ac.uk
Person Phone
Person Fax
            Warwick HRI, Wellesbourne, UK, CV35 9EF
Person Address
            HRI
Person Affiliation
Person Rolessubmitter
Person Roles Term Source REF
            replicate_quality_control
Quality Control Type
Quality Control Term Source REF
Replicate Type
Replicate Term Source REF
Normalization Type
Normalization Term Source REF
Date of Experiment
            2006-10-31
Public Release Date
PubMed ID
Publication DOI
            Author List
Publication n/a
            Title
Publication n/a
Publication Status
Publication Status Term Source REF
             Description
ExperimentA. thaliana CAGE compendim of gene expression pathogen infected cotyledon
            P-TABM-275
Protocol Name           P-TABM-273   P-TABM-274 P-TABM-272  P-TABM-277 P-TABM-279  P-TABM-280  P-TABM-278
            grow
Protocol Type           specified_biomaterial_action
                                     specified_biomaterial_action
                                                specified_biomaterial_action
                                                            nucleic_acid_extraction
                                                                       labeling                f
                                                                                   hybridizationeature_extraction
            Columbia Columbia-5Columbia-5Columbia-5Plant tissue5was of aRNA isfine powderwithand grown Hyaloperonospo
                                      ArabidopsisArabidopsisArabidopsis (7 days post-sowing) Seperatedistilled nitrogen(1µg) at
                                                  (stored at (7 oC ) post-sowing) Arrays sprayed using liquid H2O. From mirro
                                                              cotyledons cotyledons were - Spotted microarrays on Typethe follow
                                                                         ug ground to primedwere sprayed nonamers parasitic
                                                                                   were sprayed with Images were acquired fo
                                                                                                 with random with under 7* 2mL
Protocol Description -5 Arabidopsis seed were cotyledons-20 days sown on lamingtons F2 compostHyaloperonosporain athese
Protocol Parameters
Protocol Hardware
Protocol Software
Protocol Contact
Protocol Term Source REFmo           mo         mo                                             The MGED Ontology
SDRF File E-CAGE-155.sdrf.txt
            ncbitax
Term Source Name                     mo                      Ontology mo:1.3.1.1 mo
                                                The MGED ArrayExpress                          EFO
            http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html
Term Source File                                http://mged.sourceforge.net/ontologies/MGEDontology.php
                                                            http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/
                                                                       http://mged.sourceforge.net/ontologies/MGEDontology.ph
                                                                                   http://mged.sourceforge.net/ontologies/MGED
                                     http://mged.sourceforge.net/ontologies/MGEDontology.php
Term Source Version                                                    1.3.1.1
a parasitica for different time periods




 P-TABM-278
 feature_extraction
 Seperate Images were acquired for each dye.Itensities of the fluorescent signals were quantified usig imagene5(BioDiscovey Inc).The grid




 The MGED Ontology

             The MGED Ontology
             http://mged.sourceforge.net/ontologies/MGEDontology.php
imagene5(BioDiscovey Inc).The grid spots were adjusted to the array spot by thr program find spots algorithm for consistency.
orithm for consistency.

				
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