biomedical and healthCAre Data Discovery Index Ecosystem
biomedical and healthCAre Data Discovery Index Ecosystem
| Title: | Transcription profiling by array of Arabidopsis cdkf;1-2 mutant
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| dateReleased: |
08-31-2011
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| description: |
Serine phosphorylation of conserved Y1S2P3T4S5P6S7 repeats of RNA polymerase II carboxy-terminal domain (RNAPII CTD) plays a central role in the regulation of transcription and co-transcriptional RNA processing. Maintenance of CTD phosphoserine-7 mark in Arabidopsis requires the CDKF;1 kinase, which mediates in vivo activation of downstream-acting CDKD CTD kinase family. Knockout mutations of CDKF;1 lead to over 50% reduction of RNAPII CTD Ser-7 phosphorylation as early as 7 days after germination in seedlings. The transcript profiling experiment aimed at determining how early changes in CTD Ser-7 phosphorylation affect global regulation of transcription. We used Affymetrix ATH1-121501 Genome Array to compare global transcript levels in wild type and cdkf;1-2 mutant seedlings 7 days after germination. Wild type and cdkf;1-2 mutant Arabidopsis (Col-0) seedlings were grown in solid MSAR medium (Koncz, C., Martini, N., Szabados, L., Hrouda, M., Bachmair, A., and Schell, J. (1994). Specialized vectors for gene tagging and expression studies. In: Plant Molecular Biology Manual, Gelvin,S., and Schilperoort, B. (eds.), Kluwer Academic Publishers, Dordrecht-Boston-London, B2, 1-22.) containing ½ concentration of macro elements and 0.5% sucrose in Petri-dishes at 22°C, 120 mol/m2s light intensity and 8h light/16h dark period. Seedling were collected at 4h after the start of the light period in liquid nitrogen for RNA preparation.
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| privacy: |
not applicable
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| aggregation: |
instance of dataset
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| ID: |
E-GEOD-27687
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| refinement: |
raw
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| alternateIdentifiers: |
27687
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| keywords: |
functional genomics
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| dateModified: |
04-30-2015
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| availability: |
available
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| types: |
gene expression
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| name: |
Arabidopsis thaliana
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| name: |
genetic modification design
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| ID: |
A-AFFY-2
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| name: |
Affymetrix GeneChip Arabidopsis Genome [ATH1-121501]
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27687/E-GEOD-27687.raw.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| accessURL: | https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-27687/E-GEOD-27687.processed.1.zip |
| storedIn: |
ArrayExpress
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| qualifier: |
gzip compressed
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| format: |
TXT
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| accessType: |
download
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| authentication: |
none
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| authorization: |
none
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| accessURL: | https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE27687 |
| storedIn: |
Gene Expression Omnibus
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| qualifier: |
not compressed
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| format: |
HTML
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| accessType: |
landing page
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| primary: |
true
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| authentication: |
none
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| authorization: |
none
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| abbreviation: |
EBI
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| homePage: | http://www.ebi.ac.uk/ |
| ID: |
SCR:004727
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| name: |
European Bioinformatics Institute
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| homePage: | https://www.ebi.ac.uk/arrayexpress/ |
| ID: |
SCR:002964
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| name: |
ArrayExpress
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