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Sample GSM285863 Query DataSets for GSM285863
Status Public on Jan 04, 2010
Title 1-copy alpha-synuclein vs Vector at time = 4 hours (#2)
Sample type RNA
 
Channel 1
Source name Yeast 1-copy alpha-synuclein at time = 4 hours
Organism Saccharomyces cerevisiae
Characteristics w303 pump mutants (MATa can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1, pdr1::kanMX, pdr3::kanMX), containing one copy (pRS304Gal- a-syn -GFP, pRS306GAL) of alpha synuclein fused to Green Fluorescent Protein.
Extracted molecule total RNA
Extraction protocol hot phenol-chloroform extraction (Schmitt et al., 1990)
Label Cy5
Label protocol MICROMAX ASAP RNA Labeling Kit (Perkin Elmer)
 
Channel 2
Source name Yeast vector control at time = 4 hours
Organism Saccharomyces cerevisiae
Characteristics w303 pump mutants (MATa can1-100, his3-11,15, leu2-3,112, trp1-1, ura3-1, ade2-1, pdr1::kanMX, pdr3::kanMX), containing two copies of empty vector (pRS304Gal, pRS306GAL)
Extracted molecule total RNA
Extraction protocol hot phenol-chloroform extraction (Schmitt et al., 1990)
Label Cy3
Label protocol MICROMAX ASAP RNA Labeling Kit (Perkin Elmer)
 
 
Hybridization protocol Gene Expression Hybridization Kit (Agilent)
Scan protocol GenePix 4000B
Description Yeast cells were induced to a starting O.D. of 0.3 in galactose media and harvested at 0, 2, 4, and 6 hours post-induction (50 ml aliquot per timepoint). For each comparison, 3 pairs of biological replicates were hybridized to 3 different arrays. Labeling, hybridization and scanning performed by the Whitehead Institute Center for Microarray Technology.
Data processing Data were analyzed using the limma package from Bioconductor. Spots were background corrected using a normal and exponential convolutional model and an offset of 50 was added. After loess normalization by print tip, log2 ratios were calculated. Differential expression was assayed at each timepoint using a moderated t-test, corrected for false discovery rate.
 
Submission date May 01, 2008
Last update date Jan 04, 2010
Contact name Linhui Julie Su
Organization name Whitehead Institite for Biomedical Research
Lab Lindquist Lab
Street address 9 Cambridge Center
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL1210
Series (1)
GSE11633 Rescue of alpha-synuclein toxicity in a yeast model of Parkinson's disease

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (channel 1 / channel 2)

Data table
ID_REF VALUE
Q0010_01 -0.1856
Q0017_01 0.1027
Q0032_01 0.9483
Q0045_01 -0.0277
Q0050_01 -0.29
Q0055_01 -0.2567
Q0060_01 -0.2082
Q0065_01 -0.1317
Q0070_01 0.0239
Q0075_01 -0.208
Q0080_01 -0.4118
Q0085_01 -0.3967
Q0092_01 -0.0422
Q0105_01 -0.1257
Q0110_01 0.1379
Q0115_01 0.0923
Q0120_01 0.0673
Q0130_01 -0.1848
Q0140_01 0.1985
Q0142_01 0.2223

Total number of rows: 6388

Table truncated, full table size 114 Kbytes.




Supplementary file Size Download File type/resource
GSM285863.gpr.gz 622.6 Kb (ftp)(http) GPR
Processed data included within Sample table

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