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Sample GSM405144 Query DataSets for GSM405144
Status Public on Jul 01, 2009
Title YPD Replicate 2
Sample type genomic
 
Channel 1
Source name FAIRE Enriched DNA from cells growing logarithmically (vegetative) in YPD
Organism Saccharomyces cerevisiae SK1
Characteristics strain: SHy002
Growth protocol Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8.
Extracted molecule genomic DNA
Extraction protocol 100 ml of cells were fixed with 1% formaldehyde for 20 minutes at room temperature and washed twice with 1X cold PBS. The samples were then snap frozen in a dry ice/ethanol bath and stored at -80C. FAIRE was carried out as described (Hogan, Lee and Lieb 2006). Briefly, cells were thawed and lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. We conducted a phenol-chloroform extraction on the crosslinked samples (1 mg of extract) to remove proteins and protein-associated DNA. The resulting DNA samples were further purified using Zymo Clean and Concentrator kit.
Label Cy3
Label protocol ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy3 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.
 
Channel 2
Source name Genomic DNA prepped from unfixed (no Formaldehyde) sample
Organism Saccharomyces cerevisiae SK1
Characteristics strain: SHy002
Growth protocol Vegetative cells were grown in YPD (1% yeast extract, 2% peptone, 2% dextrose) to an OD600 of 0.6-0.8.
Extracted molecule genomic DNA
Extraction protocol 100 ml of UNFIXED cells were washed twice with 1X cold PBS. The cells were lysed with glass beads and the chromatin was sheared to an average size of ~800 bp by sonication as measured by agarose gel electrophoresis. We conducted a phenol-chloroform extraction on the UNFIXED samples to remove proteins. The resulting sonicated genomic DNA was precipitated with isopropanol and resuspended in 10 mM Tris-Cl pH 7.4.
Label Cy5
Label protocol ~100 ng starting material was amplified using the Whole-Genome Amplification kit (Sigma) as described (O'Geen, Nicolet, Blahnik, Green and Farnham 2006). Two micrograms of amplified DNA was labeled with Cy5 conjugated dUTP using the BioPrime Array CGH kit (Invitrogen). DNA concentration and dye incorporation were measured using a Nanodrop spectrometer.
 
 
Hybridization protocol Four micrograms of fluorescently labeled reference DNA and four micrograms of fluorescently labeled FAIRE DNA were used in the hybridization. Samples were competitively hybridized with the reference at 52C for 16 hours in a Maui hybridization chamber to yeast whole genome 4 x 44k tiling microarrays (Agilent; ~270 bp resolution).
Scan protocol The arrays were scanned with an Axon 4000B scanner, and data was extracted using GenePix 6.0 software.
Description FAIRE Meiosis Time Course - YPD Replicate 2
Data processing Probes of poor quality by visual inspection, with more than 10% saturated pixels in either channel, or with a background corrected sum of medians for both channels less than 500, were excluded from analysis (flagged as bad in GenePix). Additionally, those probes representing the mitochondrial genome were excluded. For the remaining probes, the median of the ratios (Cy5/Cy3) for each probe was converted to a log2 ratio. These log2 ratios (Cy5/Cy3) were then converted to z scores by centering at a mean of zero and scaling the standard deviation to one.
 
Submission date May 19, 2009
Last update date May 21, 2009
Contact name Sean Erik Hanlon
E-mail(s) [email protected]
Phone 919-843-3229
Organization name University of Chicago
Department Department of Human Genetics
Lab Jason Lieb
Street address 920 E. 58th Street – CLSC 515E
City Chicago
State/province IL
ZIP/Postal code 60637
Country USA
 
Platform ID GPL4131
Series (2)
GSE16163 Meiotic time course of open chromatin as measured by FAIRE
GSE18256 Meiotic time course: open chromatin and expression profile

Data table header descriptions
ID_REF
VALUE z-scored log2 ratios (Cy3/Cy5)
INV_VALUE z-scored log2 ratios (Cy5/Cy3)

Data table
ID_REF VALUE INV_VALUE
12 -1.0335 1.033496339
13 -1.70588 1.705875004
14 -0.0276075 0.027607489
15 0.0450919 -0.045091911
16 -0.355895 0.355894862
17 -0.617154 0.617153972
18 -1.18483 1.184825411
19 -0.326005 0.326004643
20 -0.643882 0.643881553
21 0.645181 -0.645181029
22 0.0581358 -0.058135825
23 0.517161 -0.517160978
24 2.57169 -2.571687739
25 1.22842 -1.228420895
26 0.0668684 -0.066868418
27 -0.314706 0.314706248
28 -0.272852 0.272851808
29 0.615279 -0.615279041
30 0.224659 -0.224658577
31 -0.376246 0.37624604

Total number of rows: 41775

Table truncated, full table size 1108 Kbytes.




Supplementary file Size Download File type/resource
GSM405144.gpr.gz 5.7 Mb (ftp)(http) GPR
Processed data included within Sample table

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