Comment[ArrayExpressAccession] E-GEOD-11071
Investigation Title C1 evolved adaptive clones M1-M5
Comment[Submitted Name] C1 evolved adaptive clones M1-M5
Publication Title Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae.
Publication Author List Kao KC, Sherlock G
Publication DOI
PubMed ID 19029899
Experimental Design transcription profiling by array
Experimental Design Term Source REF EFO
Public Release Date 2008-08-20
Experiment Description Chemostat evolution experiment C1 under glucose-limited condition at 30C. Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Genotype: Evolved clones. The genotype is not necessarily complete. Keywords: all_pairs Gene Expression profiles of adaptive clones M1-M5 in evolved conditions compared with original parents
Date of Experiment
Term Source Name EFO
Term Source Version
Term Source File
Person Last Name Sherlock Kao Sherlock
Person First Name Gavin Katy Gavin
Person Mid Initials
Person Email sherlock@genome.stanford.edu
Person Affiliation Stanford University
Person Phone 650 498 6012
Person Fax 650 724 3701
Person Address Genetics, Stanford University, 300 Pasteur Drive, Stanford, CA, USA
Person Roles submitter
Person Roles Term Source REF
Person Roles Term Accession Number
Normalization Type
Normalization Term Accession Number
Normalization Term Source REF
Replicate Type
Replicate Term Accession Number
Replicate Term Source REF
Quality Control Type
Quality Control Term Accession Number
Quality Control Term Source REF
Protocol Name P-GSE11071-1 P-GSE11071-6 P-GSE11071-5 P-GSE11071-3 P-GSE11071-2 P-GSE11071-8 P-GSE11071-4 P-GSE11071-7
Protocol Description ID_REF =
Background Pixel Correlation =
Box Bottom =
Box Left =
Box Right =
Box Top =
Error Model Used (0|1) =
Error of Log Ratio =
Feature Is Found (Green) (0|1) =
Feature Is Found (Red) (0|1) =
Feature Is Green Background Non-uniformity Outlier (0|1) =
Feature Is Green Background Population Outlier (0|1) =
Feature Is Green Non-uniformity Outlier (0|1) =
Feature Is Green Population Outlier (0|1) =
Feature Is Red Background Non-uniformity Outlier (0|1) =
Feature Is Red Background Population Outlier (0|1) =
Feature Is Red Non-uniformity Outlier (0|1) =
Feature Is Red Population Outlier (0|1) =
Feature Is Used for Global Background (0|1) =
Feature Is Used for Normalization (0|1) =
Final Processed Green Intensity =
Final Processed Red Intensity =
GNumBGUsed =
GProcessedSigError =
Green Background (mean) =
Green Background (median) =
Green Background Intensity Used =
Green Channel Saturated (0|1) =
Green Intensity (mean) =
Green Intensity (median) =
Green Intensity Is Well Above Background (0|1) =
Green Net Intensity =
Green Net Intensity Is Positive and Significant (0|1) =
Green Normalized Net Intensity =
Green Surrogate Used =
Manual Flag =
Number of Green Background Pixels =
Number of Green Inlier Pixels =
Number of Green Outlier Pixels (high intensity) =
Number of Green Outlier Pixels (low intensity) =
Number of Green Saturated Pixels =
Number of Red Background Pixels =
Number of Red Inlier Pixels =
Number of Red Outlier Pixels (high intensity) =
Number of Red Outlier Pixels (low intensity) =
Number of Red Saturated Pixels =
RNumBGUsed =
RProcessedSigError =
Red Background (mean) =
Red Background (median) =
Red Background Intensity Used =
Red Channel Saturated (0|1) =
Red Intensity (mean) =
Red Intensity (median) =
Red Intensity Is Well Above Background (0|1) =
Red Net Intensity =
Red Net Intensity Is Positive and Significant (0|1) =
Red Normalized Net Intensity =
Red Surrogate Used =
Red-Green Net Pixel Correlation =
Red-Green Normalized Net Pixel Correlation =
Red-Green Pixel Correlation =
Standard Deviation of Green Background Inlier Pixels =
Standard Deviation of Green Inlier Pixels =
Standard Deviation of Red Background Inlier Pixels =
Standard Deviation of Red Inlier Pixels =
Std Dev of Green Background Intensity =
Std Dev of Red Background Intensity =
Std Err of Green Net Intensity =
Std Err of Green Normalized Net Intensity =
Std Err of Red Net Intensity =
Std Err of Red Normalized Net Intensity =
X coordinate =
Y coordinate =
log(base 10) (P-value of Green Difference from Background) =
log(base 10) (P-value of Log Ratio) =
log(base 10) (P-value of Red Difference from Background) =
log(base 10) (REDsignal/GREENsignal) =
VALUE = log(base 2) (REDsignal/GREENsignal) Feature Extraction; The software Feature Extraction v 9.1.5 (Agilent Technology, Santa Clara, CA) was used extract data from the scanned images, and to normalize the data using the Spike-In controls.; Protocol Type = Feature Extraction; Software: type: feature extraction; Performer: Katy,,Kao not provided not provided Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC. These cultures were then used to inoculate glucose-limited chemostat cultures. Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume. To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao Chemostat Growth Conditions; Single colonies were used to inoculate overnight cultures in 2% glucose Delft minimal medium grown at 30oC. These cultures were then used to inoculate glucose-limited chemostat cultures. Chemostat vessels were inoculated with ~6x10^7 in 20ml total volume. To ensure the cells had reached steady-state, the cultures were harvested approximately 48 hours after inoculation.; Protocol Type = Growth Conditions; Performer: Katy,,Kao not provided VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
Protocol Software
Protocol Hardware
Protocol Contact
Protocol Type bioassay_data_transformation image_aquisition hybridization nucleic_acid_extraction grow labeling labeling feature_extraction
Protocol Term Source REF
Protocol Term Accession Number
Experimental Factor Name
Experimental Factor Type
Experimental Factor Term Source REF
Experimental Factor Term Accession Number
Comment[SecondaryAccession] GSE11071
Comment[GEOLastUpdateDate] 2009-03-15
Comment[GEOReleaseDate] 2008-08-19
Comment[ArrayExpressSubmissionDate] 2008-04-03
SDRF File E-GEOD-11071.sdrf.txt