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Sample GSM94301 Query DataSets for GSM94301
Status Public on Jan 30, 2006
Title S. pombe WT
Sample type genomic
 
Channel 1
Source name WT G1 phase
Organism Schizosaccharomyces pombe
Characteristics ssDNA in WT G1 phase
Treatment protocol Log phase cells were arrested in G1 phase by nitrogen starvation
Extracted molecule genomic DNA
Extraction protocol genomic DNA extracted as described on http://fangman-brewer.genetics.washington.edu/DNA_prep.html
Label Cy5
Label protocol Five micrograms of genomic DNA were digested with EcoRI for 3 hours at 37oC, followed by ethanol precipitation. The DNA was then used as template for random primed labeling at 37oC for 2.5 hours. The reaction contains 50 mM Tris-HCl, pH 6.8; 5 mM MgCl2; 10 mM -mercaptoethanol; 300 ug/ml random hexamers; 0.12 mM of each dATP, dCTP, and dGTP; 0.06 mM dTTP; 1 mM Tris-HCl, pH 8.0; 3 ul of Cy5-conjugated dUTP (Amersham) and 50 units of exonuclease deficient Klenow. The labeling reaction was performed WITHOUT denaturing the template DNA. The labeled DNA was purified through a sephadex G50 column.
 
Channel 2
Source name WT +HU early S phase
Organism Schizosaccharomyces pombe
Characteristics ssDNA in WT in early S phase in HU
Treatment protocol Log phase cells were arrested in early S phase by treatment of 12 mM HU for 3 hours at 30oC
Extracted molecule genomic DNA
Extraction protocol genomic DNA extracted as described on http://fangman-brewer.genetics.washington.edu/DNA_prep.html
Label Cy3
Label protocol Five micrograms of genomic DNA were digested with EcoRI for 3 hours at 37oC, followed by ethanol precipitation. The DNA was then used as template for random primed labeling. The reaction contains 50 mM Tris-HCl, pH 6.8; 5 mM MgCl2; 10 mM -mercaptoethanol; 300 ug/ml random hexamers; 0.12 mM of each dATP, dCTP, and dGTP; 0.06 mM dTTP; 1 mM Tris-HCl, pH 8.0; 3 ul of Cy3-conjugated dUTP (Amersham) and 50 units of exonuclease deficient Klenow. The labeling reaction was performed WITHOUT denaturing the template DNA. The labeled DNA was purified through a sephadex G50 column.
 
 
Description S. pombe WT cells (h-)
Data processing Background subtracted median values from the two channels were used to calculate the ratio of Cy3:Cy5 as the raw ratio of ssDNA (S/G1) (in table below). The raw ratio was then normalized by the total amount of ssDNA in both the G1 and S phase samples by slot blotting and hybridization experiments (Table 3 in GSE4099). The raw normalized ratios of ssDNA for all genomic locations were then smoothed over a 4kb window by Fourier transformation (Table 4 in GSE4099).
 
Submission date Jan 30, 2006
Last update date Jan 30, 2006
Contact name Bonita J Brewer
E-mail(s) bbrewer@gs.washington.edu
Phone (206) 685-2870
Fax (206) 543-0754
Organization name University of Washington
Department Genome Sciences
Lab Brewer/Raghuraman
Street address Box 357730
City Seattle
State/province WA
ZIP/Postal code 98195
Country USA
 
Platform ID GPL3398
Series (1)
GSE4099 Single stranded DNA formation during S phase in the presence of hydroxyurea in S. cerevisiae and S. pombe

Data table header descriptions
ID_REF chr_coord (kb)
VALUE log2 of PRE_VALUE
PRE_VALUE ratio ssDNA(S/G1)

Data table
ID_REF VALUE PRE_VALUE
1_2.8315 -2.4975 0.177088
1_6.0285 -2.1374 0.227292
1_12.576 -2.3861 0.191296
1_14.11 -2.3805 0.192045
1_18.3135 -2.4997 0.176817
1_20.9195 -2.4963 0.177236
1_22.0758 -2.3178 0.20058
1_23.7835 -2.3683 0.19367
1_27.558 -2.5121 0.175302
1_28.9825 -2.6485 0.159483
1_30.24 -2.2961 0.203619
1_32.45 -1.9577 0.257444
1_34.0535 -2.3666 0.193908
1_34.557 -2.4880 0.178253
1_36.075 -2.1558 0.224415
1_39.6395 -2.5182 0.174566
1_42.682 -2.4489 0.183156
1_45.059 -2.4444 0.183725
1_46.109 -2.2483 0.210465
1_52.1785 -2.1316 0.228202

Total number of rows: 4513

Table truncated, full table size 117 Kbytes.




Supplementary data files not provided

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