|
| Status |
Public on Oct 01, 2006 |
| Title |
Synthetic Lethality/slow growth with acs2-Ts8 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Control
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
Cells were obtained as a pool of heterozygous diploid Yeast Knockout strains that were sporulated and selected to yield MATa haploid progeny. The parental strain was BY4743 (from S288C), with modifications resulting in the following genotype: MATa/alpha ura3delta0 leu2delta his3delta1 lys2delta0/LYS2 met15delta0/MET15 can1delta::LEU2-MFA1pr-HIS3/CAN1 xxx::kanMX/XXX [pHT217, acs2-Ts8-CEN-URA3]. The second-site ("query") mutation had the genotype acs2::natMX. See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1 selection).
|
| Growth protocol |
Cells were grown at 33 degrees C to confluence on "Magic Marker" selection plates with G418 without uracil, histidine and clonNat. See PubMed ID 15525520.
|
| 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.
|
| |
|
| Channel 2 |
| Source name |
Experiment -- acs2-Ts8
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
As in Channel 1.
|
| Growth protocol |
Cells were grown at 33 degrees C to confluence on "Magic Marker" selection plates with G418 and cloNat without uracil and histidine. The aliquots of cells used for the two channels were split from the same source and were grown concurrently. See PubMed ID 15525520.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
As in Channel 1.
|
| Label |
Cy3
|
| Label protocol |
As in Channel 1.
|
| |
|
| |
| 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 |
See above.
|
| Data processing |
Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 3.0 or 5.1). Median intensities were used to subtract background from foreground values. The only features considered were those with ID_REF within the ranges 1:6018 (for UpTags) or 10972:16989 (for DnTags). Ratios of the background-corrected 635nm to 532nm values were obtained. Ratios were ignored when F635-B635 were less than 150. UpTag and DnTag ratios were multiplied by the normalization factors 1.8169 and 1.0615 (respectively). These normalization factors were obtained by dividing (a) the sum of F532 values over all features considered for the given tag type by (b) the corresponding sum of F635 values.
|
| |
|
| Submission date |
Jan 31, 2006 |
| Last update date |
Feb 02, 2006 |
| Contact name |
Hidekazu Takahashi |
| Organization name |
Johns Hopkins University School of Medicine
|
| Department |
High Throughput Biology Center
|
| Lab |
Jef Boeke Lab
|
| Street address |
339 Broadway Research Building, 733 North Broadway
|
| City |
Baltimore |
| State/province |
Maryland |
| ZIP/Postal code |
21205 |
| Country |
USA |
| |
|
| Platform ID |
GPL1444 |
| Series (1) |
| GSE4144 |
Synthetic lethality/slow growth with acs2-Ts8 |
|
