|
| Status |
Public on Jul 26, 2010 |
| Title |
Trivalent arsenic inhibits the functions of chaperonin complex: Sodium arsenite 1600 microM with haploids |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Control
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
yko mutant pool: haploid
|
| Growth protocol |
Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates without sodium arsenite. 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 |
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 |
Experimental
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
yko mutant pool: haploid
|
| Growth protocol |
Cells were grown at 30 degrees C to confluence on "Magic Marker" selection plates supplemented with 1600 micromolar sodium arsenite. 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 |
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. See PubMed IDs 9483801 (BY4743), 10436161 (xxx::kanMX), 11743205 (MFA1pr), 15525520 (can1, TEF1pr-URA3, selection).
|
| Data processing |
Two-channel image files were analyzed with the GenePix Pro software package (Molecular Dynamics, version 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 foreground control values (F635) were less than 400. UpTag and DnTag ratios were multiplied by the normalization factors 0.67 and 0.84 (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. For log2 transformed results, background-corrected experimental (532 nm) values below 3*sqrt(B532) were coerced to this threshold.
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| |
|
| Submission date |
Oct 03, 2006 |
| Last update date |
Aug 10, 2010 |
| Contact name |
Daniel Yuan |
| E-mail(s) |
[email protected]
|
| 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) |
| GSE5973 |
Trivalent arsenic inhibits the functions of chaperonin complex |
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