NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM285857 Query DataSets for GSM285857
Status Public on Jan 04, 2010
Title 2-copy alpha-synuclein vs Vector at time = 0 (#2)
Sample type RNA
 
Channel 1
Source name Yeast 2-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 two copies (pRS304GAL- a-syn -GFP, pRS306GAL- a-syn -GFP) 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 -0.7654
Q0017_01 0.0594
Q0032_01 -0.3399
Q0045_01 -0.2406
Q0050_01 -0.4466
Q0055_01 -1.1409
Q0060_01 -0.6218
Q0065_01 -0.7672
Q0070_01 -1.4041
Q0075_01 -1.6396
Q0080_01 -2.8585
Q0085_01 -3.4255
Q0092_01 0.1004
Q0105_01 -0.8766
Q0110_01 -0.3397
Q0115_01 0.0073
Q0120_01 -0.1981
Q0130_01 -3.1492
Q0140_01 -1.0662
Q0142_01 -0.1986

Total number of rows: 6388

Table truncated, full table size 114 Kbytes.




Supplementary file Size Download File type/resource
GSM285857.gpr.gz 643.4 Kb (ftp)(http) GPR
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap