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Sample GSM255888 Query DataSets for GSM255888
Status Public on Feb 04, 2008
Title YAP1-TAP 7.1mM MMS treatment replicate 2
Sample type genomic
 
Channel 1
Source name YAP1-TAP, 7.1mM MMS, input DNA
Organism Saccharomyces cerevisiae
Characteristics Yeast BY4741 strain with YAP1-TAP
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde, lysed, and sonicated to shear DNA. DNA fragments bound by the tagged TF were enriched by immunoprecipitation with an anti-TAP antibody (Open Biosystems). Afer reversal of crosslinking, DNA fragments were purified by phenol chloroform extraction
Label Cy3
Label protocol non-antibody enriched DNA sample was amplified by LM-PCR using a Cy3 label.
 
Channel 2
Source name YAP1-TAP, 7.1mM MMS, anti-TAP enriched
Organism Saccharomyces cerevisiae
Characteristics Yeast BY4741 strain with YAP1-TAP
Extracted molecule genomic DNA
Extraction protocol Cells were fixed with 1% formaldehyde, lysed, and sonicated to shear DNA. DNA fragments bound by the tagged TF were enriched by immunoprecipitation with an anti-TAP antibody (Open Biosystems). Afer reversal of crosslinking, DNA fragments were purified by phenol chloroform extraction
Label Cy5
Label protocol Enriched DNA was amplified and Cy5-labeled by ligation-mediated PCR (LM-PCR).
 
 
Hybridization protocol Cy-3 and Cy-5 labeled samples were mixed with hybridization buffer (Agilent In Situ Hybridization Kit) and co-hybridized to the Yeast Whole Genome Tiling Array (G4486A, Agilent Technologies). Slides were hybridized for 17h at 60 degree Celcius in a rotating oven, and washed
Scan protocol Scanned on an GenePix 4000A scanner (Axon Instruments) at a 10.0 um resolution
Images were quantified using GenePix Pro 6.0 software (Axon Instruments)
Description yeast cells treated with 7.1mM MMS, enriched DNA compared to input genoimc DNA.
Data processing Background subtraction. Background-adjusted log ratios were then corrected for cyanine-dye dependent bias using Loess normalization
 
Submission date Jan 10, 2008
Last update date Feb 04, 2008
Contact name Kai Tan
Organization name University of California San Diego
Department Bioengineering
Street address 9500 Gilman Drive
City La Jolla
State/province CA
ZIP/Postal code 92093
Country USA
 
Platform ID GPL3737
Series (1)
GSE10146 A systems approach to delineate functions of YAP family members

Data table header descriptions
ID_REF
VALUE log10(Cy5signal/Cy3signal) per feature (normalized signals used)
CH1_SIG_MEAN mean normalized foreground signal from Cy3 channel
CH2_SIG_MEAN mean normalized foreground signal from Cy5 channel

Data table
ID_REF VALUE CH1_SIG_MEAN CH2_SIG_MEAN
6181 1.245 13.2 232.9
38946 1.1603 32.5 470.1
16759 1.0556 935.4 10632.4
13899 0.9049 1841 14788.8
37217 0.8789 786.1 5948.2
24422 0.8774 26.8 201.9
43531 0.816 80.8 528.9
16794 0.8101 83.2 537.4
14855 0.796 73.3 458.4
41801 0.7935 8.4 52.4
7006 0.7878 1305.8 8010.4
31923 0.7574 11.8 67.3
19034 0.7553 7.1 40.6
17972 0.7522 15.1 85.5
10158 0.7486 14.7 82.3
2312 0.7467 24.7 137.8
16545 0.7369 1741.6 9503
13361 0.736 38.7 210.5
36803 0.7325 25.5 137.8
30502 0.7322 5.1 27.8

Total number of rows: 44290

Table truncated, full table size 1087 Kbytes.




Supplementary file Size Download File type/resource
GSM255888.gpr.gz 5.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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