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Sample GSM255955 Query DataSets for GSM255955
Status Public on Feb 04, 2008
Title YAP6-TAP 4.7mM MMS treatment replicate 1
Sample type genomic
 
Channel 1
Source name YAP6-TAP, 4.7mM MMS, input DNA
Organism Saccharomyces cerevisiae
Characteristics Yeast BY4741 strain with YAP6-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 YAP6-TAP, 4.7mM MMS, anti-TAP enriched
Organism Saccharomyces cerevisiae
Characteristics Yeast BY4741 strain with YAP6-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 4.7mM MMS, enriched DNA compared to input genomic 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 1.2057 47.9 769.5
23217 1.1384 6.2 85.2
8049 1.0144 8.2 84.5
36803 0.9733 97.5 916.5
27948 0.954 10.9 98.3
43531 0.9383 109.4 948.8
17972 0.9169 32.2 265.9
33003 0.9002 465.7 3701.2
38826 0.8435 9.5 66
19034 0.8343 15 102.4
40826 0.7945 2309.6 14388.5
28785 0.7933 10.2 63.2
19501 0.788 16.8 103.1
32348 0.7834 148.3 900.7
6742 0.7832 129.5 786
33449 0.7737 13.2 78.3
32876 0.7653 487.8 2841
1824 0.758 8.2 46.7
38946 0.7492 94.5 530.4
5883 0.7327 298.8 1614.6

Total number of rows: 44290

Table truncated, full table size 1099 Kbytes.




Supplementary file Size Download File type/resource
GSM255955.gpr.gz 6.0 Mb (ftp)(http) GPR
Processed data included within Sample table

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