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Sample GSM160746 Query DataSets for GSM160746
Status Public on Aug 14, 2007
Title SP HU syn WT harvested at 000 min Bio_1_R2
Sample type genomic
 
Channel 1
Source name Fission yeast cells
Organism Schizosaccharomyces pombe
Characteristics Schizosaccharomyces pombe wild type (WT) cells were synchronized by treating the cells with 8 mM Hydroxyurea (HU+) for 3 hrs, and the cells were released in HU free media and harvested after 0 min.
Growth protocol Yeast cells were cultured at 30 degree centigrade.
Extracted molecule genomic DNA
Extraction protocol DNA of the cells were extracted as describled in materials and metholds.
Label Cy5
Label protocol Sheared DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture¡¯s instruction. Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy5 (Amersham, Buckinghamshire, UK)
 
Channel 2
Source name Fission yeast arrested cells with 8 mM Hydroxyurea for 3 hrs.
Organism Schizosaccharomyces pombe
Characteristics Reference DNA was obtained by extracting the DNA from the cells treated with 8 mM HU for 3 hrs.
Extracted molecule genomic DNA
Extraction protocol DNA of the cells were extracted as describled in materials and metholds.
Label Cy3
Label protocol Sheared DNA was random-priming labeled with amino-allyl-dUTP (aa-dUTP) using the BioPrime DNA Labeling kit (Invitrogen Corporation, Carlsbad, CA) according the manufacture¡¯s instruction. Labeled DNA was extracted with phenol/chloroform/isoamyl alcohol and precipitated with ethanol or siopropanol. The labeled DNA was then coupled with cyanine dyes Cy3 (Amersham, Buckinghamshire, UK)
 
 
Hybridization protocol Samples were mixed with DIG Easy Hyb buffer (Roche) and Herring Sperm DNA (Invitrogen) before applying to MAUI mixer-slide assembly. The slides were hybridized overnight for 16 hours at 42¡ãC under MAUI system (BioMicro). Hybridized slides were washed consecutively in 2¡Á SSC/0.1% SDS for 1 min, 1¡Á SSC for 4 min, 0.2¡Á SSC for 4 min, and 0.05¡Á SSC for 1 min, and then spin-dried before scanning.
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software.
Description Schizosaccharomyces pombe cells synchronized with 8 mM HU for 3 hrs and released in HU free media at 0 time points vs Schizosaccharomyces pombe cells synchronized with 8 mM HU for 3 hrs.
Data processing Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000A fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 4.0 analysis software. After background correction and removal of flagged values, features with low intensity (F/B<2 at either 635 or 532 channel) were removed. Meidans of log base 2 expression ratios were given in the data table.
 
Submission date Feb 07, 2007
Last update date Aug 14, 2007
Contact name Majid Eshaghi
E-mail(s) meshaghi@hotmail.com
Organization name Genome Institute of Singapore
Department Bilogical Investigation
Lab System Biology
Street address Biopolis
City Singapore
State/province Singapore
ZIP/Postal code 138672
Country Singapore
 
Platform ID GPL1932
Series (1)
GSE6977 Genome-wide Profiling of DNA Replication Timing in pombe.

Data table header descriptions
ID_REF
VALUE same as UNF_VALUE but with flagged values removed
CH1_Median CH1 (F635) median fluorescence intensity
CH1_BKD CH1 (B635) background median fluorescence intensity
CH2_Median CH2 (F532) median fluorescence intensity
CH2_BKD CH2 (B532) background median fluorescence intensity
CH1_Median - CH1_BKD Channel 1 median signal - absolute intensity
CH2_Median - CH2_BKD Channel 2 median signal - absolute intensity
Flags Denotes which features met our filtering criterion. A negative value means that the feature did not have at least 60% of its pixels greater than two standard deviations over the background intensity.
2Fold_F/B Denotes which features met our filtering criterion. Zero value means that the feature whose intensity did not pass either F635/B635>=2 or F532/B532>=2, that is, low-intensity features.
UNF_VALUE Median of log2 ratio defined by CH1/ CH2

Data table
ID_REF VALUE CH1_Median CH1_BKD CH2_Median CH2_BKD CH1_Median - CH1_BKD CH2_Median - CH2_BKD Flags 2Fold_F/B UNF_VALUE
c1348_1000011 0.583038 9818 106 6303 98 9712 6205 0 1 0.583038
c1348_1000012 0.584963 4255 99 2888 87 4156 2801 0 1 0.584963
c1348_1000021 0.594549 6211 99 4161 87 6112 4074 0 1 0.594549
c1348_1000022 0.511974 3124 108 2230 98 3016 2132 0 1 0.511974
c1348_1000031 0.535058 7872 102 5767 98 7770 5669 0 1 0.535058
c1348_1000032 0.441483 3557 98 2790 85 3459 2705 0 1 0.441483
c1348_1000041 0.484396 3396 104 2389 100 3292 2289 0 1 0.484396
c1348_1000042 0.396159 2787 103 2288 161 2684 2127 0 1 0.396159
c1348_1000051 0.423309 964 104 745 99 860 646 0 1 0.423309
c1348_1000052 0.0356239 780 99 672 96 681 576 0 1 0.0356239
c1348_1000061 0.516015 1934 108 1412 107 1826 1305 0 1 0.516015
c1348_1000062 0.594549 2369 106 1575 106 2263 1469 0 1 0.594549
c1348_1000071 0.441483 2602 99 2001 97 2503 1904 0 1 0.441483
c1348_1000072 0.531069 3717 110 2539 102 3607 2437 0 1 0.531069
c1348_1000081 0.493647 3657 104 2579 99 3553 2480 0 1 0.493647
c1348_1000082 0.43082 3295 94 2620 112 3201 2508 0 1 0.43082
c1348_1000091 0.591679 3504 100 2332 92 3404 2240 0 1 0.591679
c1348_1000092 0.503858 3193 99 2263 147 3094 2116 0 1 0.503858
c1348_1000101 0.257011 855 92 750 56 763 694 0 1 0.257011
c1348_1000102 0.377401 876 97 747 104 779 643 0 1 0.377401

Total number of rows: 9858

Table truncated, full table size 588 Kbytes.




Supplementary file Size Download File type/resource
GSM160746.gpr.gz 853.3 Kb (ftp)(http) GPR
Processed data included within Sample table

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