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Sample GSM285856 Query DataSets for GSM285856
Status Public on Jan 04, 2010
Title 1-copy alpha-synuclein vs Vector at time = 0 (#2)
Sample type RNA
 
Channel 1
Source name Yeast 1-copy alpha-synuclein at time = 0
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 = 0
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 -0.2918
Q0017_01 0.3609
Q0032_01 -0.1114
Q0045_01 -0.0881
Q0050_01 -0.2538
Q0055_01 -0.8735
Q0060_01 -0.3737
Q0065_01 -0.5304
Q0070_01 -1.0065
Q0075_01 -1.1216
Q0080_01 -2.5418
Q0085_01 -3.0387
Q0092_01 0.1033
Q0105_01 -0.4877
Q0110_01 -0.1258
Q0115_01 0.3666
Q0120_01 0.0873
Q0130_01 -2.6473
Q0140_01 -0.8755
Q0142_01 0.0413

Total number of rows: 6388

Table truncated, full table size 114 Kbytes.




Supplementary file Size Download File type/resource
GSM285856.gpr.gz 623.1 Kb (ftp)(http) GPR
Processed data included within Sample table

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