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Series GSE2583 Query DataSets for GSE2583
Status Public on Apr 29, 2005
Title Genome_Wide_Oscillations_in_Yeast
Organism Saccharomyces cerevisiae
Experiment type Expression profiling by array
Summary In order to test the idea that the cell is an attractor and to examine in detail the connectivity relationships among genes, it was essential to have a very reproducible and precise biological system. Oscillations in respiratory activity in budding yeast and other organisms have been known for many years. This benchmark oscillation is now shown to be a global manifestation of a genome wide oscillation in transcription. Using Affymetrix S98 chips, the patterns of gene expression were followed by sampling at 4-minute intervals through three cycles of the DO oscillation. Phase assignments were made based on the dissolved oxygen cycle. Two different cultures were sampled and a total of 68 RNA samples were prepared. Choices of samples for microarray analysis were based on RNA quality, consistent with having a complete set of 32 samples chosen to represent three cycles of the DO oscillation. Ten were chosen from the first experiment and 22 from the second experiment. Analysis using singular value decomposition recognizes a small difference in cycle time between the two experiments. Strictly speaking, there are no replicates. The time of maximum gene expression in the cycle was determined by phase grouping and averaging gene expression in the three replicates, assigning the phase of maximum expression to each transcript then examining how well this assignment is reproduced through the three cycles. We found that 5329 expressed genes were present in at least one sample and used them in our analysis.
The correct order is GSM48136, GSM48137, GSM48138, GSM48139, GSM48140, GSM48131, GSM48132, GSM48133, GSM48134, GSM48135, GSM48149, GSM48150, GSM48141, GSM48151, GSM48142, GSM48143, GSM48144, GSM48145, GSM48146, GSM48147, GSM48148, GSM48160, GSM48161, GSM48162, GSM48157, GSM48158, GSM48152, GSM48159, GSM48153, GSM48154, GSM48155, GSM48156
Keywords: time-course
Contributor(s) Klevecz RR, Bolen JL, Forrest GL, Murray DB
Citation(s) 14734811
Submission date Apr 26, 2005
Last update date Jul 01, 2016
Contact name Robert R Klevecz
Phone 6263018348
Organization name Beckman Research Institute of the City of Hope
Department Biology
Lab Cellular Dynamics
Street address 1450 E. Duarte Rd.
City Duarte
State/province CA
ZIP/Postal code 91010
Country USA
Platforms (1)
GPL90 [YG_S98] Affymetrix Yeast Genome S98 Array
Samples (32)
GSM48131 Genome wide transcriptional oscillation gates DNA replication AFFY1_1
GSM48132 Genome wide transcriptional oscillation gates DNA replication AFFY1_2
GSM48133 Genome wide transcriptional oscillation gates DNA replication AFFY1_3
BioProject PRJNA91991

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE2583_correctly_ordered_Klevecz_GEO_time_series_data.txt 1.6 Mb (ftp)(http) TXT

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