|
| Status |
Public on Jun 12, 2008 |
| Title |
Genetic interactions involving the esa1-531 query mutation at 31 degrees C |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Cells selected for the query mutation
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Query mutation: esa1-delta::natMX with esa1-531 (ts allele) in URA3 CEN plasmid
|
| Growth protocol |
Growth medium: +Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 31 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: esa1-delta::natMX with esa1-531 (ts allele) in URA3 CEN plasmid
|
| Growth protocol |
Growth medium: -Nourseothricin (SC-His, -Leu-Arg+Canavanine+G418, -Ura)
Growth temperature: 31 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 esa1-531 xxxN vs xxxN cells at 31 degrees C
|
| 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 |
|
