|
| Status |
Public on Jun 15, 2006 |
| Title |
HDDP_shaker_rep2 |
| Sample type |
genomic |
| |
|
| Source name |
Homozygous diploid deletion pool, grown in shaker
|
| Organism |
Saccharomyces cerevisiae |
| Characteristics |
A pool of all homozygous diploid deletion strains, derived from the parental strain BY4743 (MAT a/alpha his3D1, leu2D, met15D ura3D)
|
| Biomaterial provider |
Invitrogen
|
| Growth protocol |
Culture was grown for 18 hours at 30 C in a rotating wall vessel placed in a gyrorotatory shaker set at 90 rpm
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was prepared from yeast cultures using the MasterPure yeast DNA purification kit (Gentra Systems, Minneapolis, Mass.)
|
| Label |
Biotin
|
| Label protocol |
The uptag and downtag barcodes from all deletion cassettes were amplified from the genomic DNA of the homozygous deletion pool, using biotinylated primers specific to the universal sequences at the end of each unique barcode region. The four primer sequences were U1 (GATGTCCACGAGGTCTCT), U2 (CGTACGCTGCAGGTCGAC), D1 (CGGTGTCGGTCTCGTAG), and D2 (ATCGATGAATTCGAGCTCG).
|
| |
|
| Hybridization protocol |
1.2 ug of the uptag and downtag products were combined with 200 uM unlabeled primers (U1, U2, D1, D2) and hybridized to a TAG 3 array. The sample volume was brought to 200 l in 6× SSPE-T, boiled for 2 min, and then allowed to cool on ice. Before hybridization, the TAG 3 chip was washed for 10 min with 6× SSPE-T. The sample was then hybridized to the chip for 16 h at 42°C. Following hybridization, the chip was washed two times with six changes of 6× SSPE-T, then stained with streptavidin–phycoerythrein for 10 min at 42°C, and washed two times with five changes of 6× SSPE-T
|
| Scan protocol |
Chip was scanned at 560 nm using a GeneChip scanner (Affymetrix, Santa Clara, Calif.). The hybridization intensities for each of the array elements were determined using Affymetrix GeneChip software.
|
| Description |
Saccharomyces cerevisiae homozygous diploid deletion pool grown in a rotating wall vessel (RWV) for 18 hours in a shaker
|
| Data processing |
Affymetrix GeneChip software
|
| |
|
| Submission date |
Jun 15, 2005 |
| Last update date |
Oct 28, 2005 |
| Contact name |
Timothy Hammond |
| E-mail(s) |
thammond@tulane.edu
|
| Organization name |
Tulane University Health Sciences Center
|
| Department |
Department of Medicine, Nephrology Section, SL-45
|
| Street address |
1430 Tulane Ave
|
| City |
New Orleans |
| State/province |
LA |
| ZIP/Postal code |
70115 |
| Country |
USA |
| |
|
| Platform ID |
GPL2544 |
| Series (1) |
| GSE2818 |
Gene expression and survival changes in Saccharomyces cerevisiae during suspension culture. |
|
