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Sample GSM356385 Query DataSets for GSM356385
Status Public on May 07, 2009
Title Yeast_gene_order_36d_rep1
Sample type genomic
 
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)
 
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.
 
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

Data table header descriptions
ID_REF
VALUE normalized log2 (Median of Ratios) R/G

Data table
ID_REF VALUE
302 -0.131
303 -0.209
304 0.317
305 -0.089
306 -0.016
307 NULL
308 0.507
309 -0.092
310 0.18
311 -0.299
312 NULL
313 -0.076
314 0.084
315 NULL
316 -0.037
317 0.45
318 0.092
319 0.361
320 -1.535
321 0.307

Total number of rows: 15397

Table truncated, full table size 174 Kbytes.




Supplementary file Size Download File type/resource
GSM356385.gpr.gz 1.8 Mb (ftp)(http) GPR
Processed data included within Sample table

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