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E-GEOD-13532 - RNAi knockdown of NMD in D Melanogaster

Status
Submitted on 8 November 2008, released on 18 May 2010, last updated on 1 May 2014
Organism
Drosophila melanogaster
Samples (12)
Array (1)
Protocols (7)
Description
Two core factors of the NMD machinery in D. melanogaster, Upf1 and Upf2, were knocked down using RNAi, as described in Rehwinkel et al. (2005) RNA, PMID: 16199763. Each of the two knockdowns were compared to mock RNAi knockdowns as described in Blanchette et al. (2005) Genes Dev, PMID: 15937219 in a dual channel experiment, using a custom splice-junction microarray design, see Blanchette et al. (2005), PMID: 15937219. The aim of the experiment was to identify which isoforms of alternatively spliced genes were affected by NMD knockdown and thereby gain insight into the NMD mechanism in Drosophila. The samples were hybridized in a dual channel setup, to custom designed Splice-Junction arrays manufactured by Agilent. A total of 6 independent knockdowns (3 Upf1 and 3 Upf2) were generated and hybridized to 6 different arrays. On each array a control sample was hybridized as well. The control sample is a pool of 3 independent mock RNAi knockdowns.
Experiment type
transcription profiling by array 
Contacts
Kasper Daniel Hansen <khansen@compbio.berkeley.edu>, Ed R Green, Kasper D Hansen, Macro Blanchette
Citation
Genome-wide identification of alternative splice forms down-regulated by nonsense-mediated mRNA decay in Drosophila. Hansen KD, Lareau LF, Blanchette M, Green RE, Meng Q, Rehwinkel J, Gallusser FL, Izaurralde E, Rio DC, Dudoit S, Brenner SE.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-13532.idf.txt
Sample and data relationshipE-GEOD-13532.sdrf.txt
Raw data (1)E-GEOD-13532.raw.1.zip
Processed data (1)E-GEOD-13532.processed.1.zip
Array designA-GEOD-7508.adf.txt
R ExpressionSetE-GEOD-13532.eSet.r
Links