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Status |
Public on May 07, 2009 |
Title |
Yeast_gene_order_36d_rep1 |
Sample type |
genomic |
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Channel 1 |
Source name |
genomic DNA 36d
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
genomic DNA tetrad 36 spore d (tetrad derived from S90 x Y101)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Twenty-milliliter cultures of each sample were grown in YPD medium (yeast extract 10g/L, peptone 20 g/L, and 2% dextrose) to OD600 greater than one. Cells were collected and resuspended in TE (700 μL of 200mM Tris, 50mM EDTA, pH 8) and frozen overnight. To digest cell walls, the cells were resuspended in 535 μL of 20mg/ml Zymolyase, 1.2 M Sorbitol, 20mM HEPES (pH 7.5) and incubated for 60 minutes at 37°C. Collected cells were resuspended in TE + 10 mg/ml RNaseA at 65°C for 30 minutes. 200 μL 5M potassium acetate was added and cells were incubated on ice for 1 hour. The lysed cells were then centrifuged at 14K rpm for 10 minutes to pellet debris (Sovall Biofuge Pico). Genomic DNA was ethanol precipitated from the supernatant and resuspended in 200 μL TE (pH 8). The solution was then sonicated to fragment DNA to an average size of ~ 500 bp. DNA was purified using YeaStar Genomic DNA Kit (Zymo Research, cat # D2002) and concentrations were determined by absorption spectroscopy with PicoGreen (Invitrogen)
|
Label |
Cy5
|
Label protocol |
Samples and references were labeled using BioPrime Array CGH Genomic Labeling Module (Invitrogen) (see Gabriel et al., 2006)
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|
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Channel 2 |
Source name |
genomic DNA S288C
|
Organism |
Saccharomyces cerevisiae |
Characteristics |
genomic DNA S288C (reference strain)
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Twenty-milliliter cultures of each sample were grown in YPD medium (yeast extract 10g/L, peptone 20 g/L, and 2% dextrose) to OD600 greater than one. Cells were collected and resuspended in TE (700 μL of 200mM Tris, 50mM EDTA, pH 8) and frozen overnight. To digest cell walls, the cells were resuspended in 535 μL of 20mg/ml Zymolyase, 1.2 M Sorbitol, 20mM HEPES (pH 7.5) and incubated for 60 minutes at 37°C. Collected cells were resuspended in TE + 10 mg/ml RNaseA at 65°C for 30 minutes. 200 μL 5M potassium acetate was added and cells were incubated on ice for 1 hour. The lysed cells were then centrifuged at 14K rpm for 10 minutes to pellet debris (Sovall Biofuge Pico). Genomic DNA was ethanol precipitated from the supernatant and resuspended in 200 μL TE (pH 8). The solution was then sonicated to fragment DNA to an average size of ~ 500 bp. DNA was purified using YeaStar Genomic DNA Kit (Zymo Research, cat # D2002) and concentrations were determined by absorption spectroscopy with PicoGreen (Invitrogen)
|
Label |
Cy3
|
Label protocol |
Samples and references were labeled using BioPrime Array CGH Genomic Labeling Module (Invitrogen) (see Gabriel et al., 2006)
|
|
|
|
Hybridization protocol |
DNA was hybridized to the microarrays as previously described (see Iyer et al., 2001). In all cases, S288C was used as the reference for competitive hybridization.
|
Scan protocol |
Images were acquired using a GenePix 4000B scanner and Genepix software (Axon Instruments)
|
Description |
Gene order 36d rep1
|
Data processing |
Data were uploaded to the UNC Microarray Database and retrieved as the log2 normalized ratio of (median intensity of sample pixels / median intensity of reference pixels). Only spots with a regression correlation >0.6 (i.e. those comprised of pixels with consistent ratio values). Spots that either failed from PCR or that were flagged in Genepix were not downloaded. Data were then z-score transformed such that the mean of all spots became 0 and the standard deviation became 1.
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|
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Submission date |
Dec 27, 2008 |
Last update date |
May 06, 2009 |
Contact name |
Jason D. Lieb |
E-mail(s) |
[email protected]
|
Phone |
919-843-3228
|
Fax |
919-962-1625
|
Organization name |
The University of North Carolina-Chapel Hill
|
Department |
Biology and Carolina Center for Genome Sciences
|
Lab |
Jason Lieb Lab and Todd Vision Lab
|
Street address |
Department of Biology, #3280, Coker Hall
|
City |
Chapel Hill |
State/province |
NC |
ZIP/Postal code |
27599-3280 |
Country |
USA |
|
|
Platform ID |
GPL4414 |
Series (1) |
GSE14223 |
Systematic identification of balanced transposition polymorphisms in Saccharomyces cerevisiae |
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