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E-GEOD-27687 - Transcription profiling by array of Arabidopsis cdkf;1-2 mutant

Status
Released on 31 August 2011, last updated on 30 April 2015
Organism
Arabidopsis thaliana
Samples (6)
Array (1)
Protocols (9)
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.
Experiment types
transcription profiling by array, genetic modification design
Contacts
Csaba Koncz <koncz@mpiz-koeln.mpg.de>, Bruno Huettel, Mohsen Hajheidari
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-27687.idf.txt
Sample and data relationshipE-GEOD-27687.sdrf.txt
Raw data (1)E-GEOD-27687.raw.1.zip
Processed data (1)E-GEOD-27687.processed.1.zip
Array designA-AFFY-2.adf.txt
Links