GEA IDF/SDRF/ADF Examples
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Comment[GEAAccession]E-GEAD-369
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MAGE-TAB Version1.1
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Investigation Title
Transcriptional profiling of Arabidopsis leaves exposed to elevated temperature
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Experiment Description
We investigated genome-wide changes in mRNA transcription in Arabidopsis thaliana leaves exposed to brief perids of elevated temperature (37 degree_C) stress. To this end, we hybridized poly A RNA from Arabidopsis leaves with and without heat stress on Affymetrix GeneChip Arabidopsis Genome. Two biological replicates were analyzed.
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Experimental Designstimulus or stress design
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Experimental Factor Name
temperature
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Experimental Factor Type
temperature
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Person Last NameTest
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Person First NameTarou
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Person AffiliationDDBJ Center, National Institute of Genetics
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Person Rolessubmitter
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PubMed ID29040613
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Protocol NameP-GEAD-535P-GEAD-536P-GEAD-537P-GEAD-538P-GEAD-539P-GEAD-540
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Protocol Typesample collection protocol
nucleic acid extraction protocol
nucleic acid labeling protocol
nucleic acid hybridization to array protocol
array scanning and feature extraction protocol
normalization data transformation protocol
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Protocol Description
Plants were sown on GM medium (MS salts + 1% sucrose) and grown for 9 days under continuous white light at 22 degrees celsius.
Approximately 0.3 g of stress-treated leaves or the corresponding control leaves were pulverized in liquid nitrogen with a mortar and pestle. Total RNA was isolated from the resulting frozen powder using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) followed by RNeasy mini spin columns (Qiagen) with oncolumn DNase I treatment. The reagents and kit were used according to the manufacturer's instructions. RNA integrity was examined with an Agilent Bioanalyzer 2100 (Agilent Technologies).
As per Affymetrix instructions.
As per Affymetrix instructions.
Standard Affymetrix array scanning and MAS5 extraction.
Standard affymetrix protocols.
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SDRF FileE-GEAD-369.sdrf.txt
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Comment[Number of channel]
single-channel
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Comment[Array Design REF]
A-AFFY-2
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Comment[AEExperimentType]
transcription profiling by array
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Comment[BioProject]PRJDB3647
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Comment[Public Release Date]
2018-06-22
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Comment[Last Update Date]
2018-06-22
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