NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM246453 Query DataSets for GSM246453
Status Public on Jun 12, 2008
Title Genetic interactions involving the eaf6 query mutation
Sample type genomic
 
Channel 1
Source name Cells selected for the query mutation
Organism Saccharomyces cerevisiae
Characteristics Query mutation: eaf6-delta::URA3
Growth protocol Growth medium: -Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520.
Label Cy3
Label protocol UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458.
 
Channel 2
Source name A matched aliquot of cells, grown in parallel but without selection for the query mutation
Organism Saccharomyces cerevisiae
Characteristics Query mutation: eaf6-delta::URA3
Growth protocol Growth medium: +Ura (SC-His, -Leu-Arg+Canavanine+G418)
Growth temperature: 30 degrees C
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and grown to yield MATa haploid progeny. See PubMed ID 16487579 for an overview and PubMed IDs 17189863 and 15525520 for detailed experimental protocols.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was prepared by extraction with phenol-chloroform and ethanol-precipitated. See PubMed ID 15525520.
Label Cy5
Label protocol UpTag and DnTag sequences were amplified from genomic DNA by asymmetric PCR using labeled primers. See PubMed ID 15994458.
 
 
Hybridization protocol Labeled extracts were hybridized overnight to microarray slides at 42 degrees C. See PubMed ID 15994458.
Scan protocol Images were acquired with a GenePix 4000B scanner.
Description Matched comparison of the viability of eaf6 xxxN vs xxxN cells
Data processing Paired image files were analyzed with the GenePix Pro software package (MDS Analytical Technologies, version 5.1). Feature intensities were quantified as the 'F532 Median - B532' or 'F635 Median - B635' values. The two channels were compared using the log2 ratio. Global intensity normalization factors were specific to the type of gene-specific probe (UpTag or DnTag) and were calculated as the log2 ratio of total signal intensity in features 1:6018 (UpTag) or 10972:16989 (DnTag). Ratios were ignored when intensities of the control features [635] were less than 400.
 
Submission date Dec 04, 2007
Last update date Aug 14, 2011
Contact name Daniel Yuan
E-mail(s) dyuan@jhmi.edu
Phone 410-502-1877
Fax 401-502-1872
Organization name Johns Hopkins Univ School of Medicine
Department Molecular Biology and Genetics
Lab Jef Boeke
Street address 733 N. Broadway, Suite 351
City Baltimore
State/province MD
ZIP/Postal code 21205-1832
Country USA
 
Platform ID GPL1444
Series (1)
GSE9771 A comprehensive synthetic genetic interaction network governing yeast histone acetylation and deacetylation

Data table header descriptions
ID_REF
VALUE normalized log2 ratio (Cy3/Cy5)

Data table
ID_REF VALUE
1
2 1.11
3
4 0.20
5 -0.24
6
7 0.26
8 1.90
9 -1.30
10 -2.84
11
12
13 0.48
14 0.44
15
16 -1.46
17 -0.55
18 -0.65
19 1.73
20

Total number of rows: 22575

Table truncated, full table size 184 Kbytes.




Supplementary file Size Download File type/resource
GSM246453.gpr.gz 1.8 Mb (ftp)(http) GPR
GSM246453.tif.gz 24.1 Mb (ftp)(http) TIFF
Processed data included within Sample table

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