E-GEOD-4275 - Global Identification of Noncoding RNAs in S. cerevisiae

Status
Submitted on 20 February 2006, released on 28 February 2006, last updated on 27 March 2012
Organism
Saccharomyces cerevisiae
Samples (8)
Array (1)
Protocols (3)
Description
Genome-wide detection of novel non-coding RNAs in S. cerevisiae by modulating an RNase P pathway through the depletion of a component RPP1. Nearly 400,000 36-mer oligonucleotide probes, tiling the entire yeast genome including the mitochondrial chromosome with an average gap of 10 bases between two consecutive probes, were synthesized on glass slides using a mask-less array synthesizer. RNA samples for hybridizing to the arrays were extracted from a conditional lethal allele of S. cerevisiae created by placing the RPP1 gene under control of GAL10 promoter. It allowed the expression of RPP1 in galactose-containing culture medium but suppressed its expression in glucose-containing medium. A wild-type isogenic strain was used as a control. Both strains were initially grown in galactose-containing medium and subsequently transferred and resuspended into glucose-containing medium. Eight arrays were hybridized with RNA extracted from the Rpp1-depleted cells at 0, 4, 7, 12, 16, 21, 30h, and the control cell at 30h, after initial transfer to glucose-containing medium.
Experiment type
unknown experiment type 
Contacts
Waraporn Tongprasit <wtongprasit@mail.arc.nasa.gov>, Chen-shan Chin, Himanshu Sethi, Manoj P Samanta, Viktor Stolc
Citation
MIAME
PlatformsProtocolsFactorsProcessedRaw
Files
Investigation descriptionE-GEOD-4275.idf.txt
Sample and data relationshipE-GEOD-4275.sdrf.txt
Processed data (1)E-GEOD-4275.processed.1.zip
Array designA-GEOD-3471.adf.txt
Links