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Sample GSM160781 Query DataSets for GSM160781
Status Public on Aug 14, 2007
Title SP HU syn Cds1 harvested at 015 min Bio_2
Sample type genomic
 
Channel 1
Source name Fission yeast cells
Organism Schizosaccharomyces pombe
Characteristics Schizosaccharomyces pombe Cds1 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 15 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 1.70443 23103 135 7110 111 22968 6999 0 1 1.70443
c1348_1000012 1.64293 12278 138 4004 111 12140 3893 0 1 1.64293
c1348_1000021 1.73769 21286 189 6503 125 21097 6378 0 1 1.73769
c1348_1000022 1.46728 11833 126 4452 108 11707 4344 0 1 1.46728
c1348_1000031 1.58352 18841 150 6232 115 18691 6117 0 1 1.58352
c1348_1000032 1.53007 9433 141 3279 115 9292 3164 0 1 1.53007
c1348_1000041 1.47457 6349 165 2356 132 6184 2224 0 1 1.47457
c1348_1000042 1.54893 7397 150 2661 125 7247 2536 0 1 1.54893
c1348_1000051 1.43723 2888 143 1157 111 2745 1046 0 1 1.43723
c1348_1000052 1.20789 2781 113 1230 103 2668 1127 0 1 1.20789
c1348_1000061 1.51046 5038 158 1840 124 4880 1716 0 1 1.51046
c1348_1000062 1.47457 4477 177 1697 124 4300 1573 0 1 1.47457
c1348_1000071 1.51803 6255 150 2271 128 6105 2143 0 1 1.51803
c1348_1000072 1.40218 7147 128 3013 116 7019 2897 0 1 1.40218
c1348_1000081 1.84639 9780 119 2859 108 9661 2751 0 1 1.84639
c1348_1000082 1.82375 10861 171 3125 136 10690 2989 0 1 1.82375
c1348_1000091 1.66038 11113 138 3567 113 10975 3454 0 1 1.66038
c1348_1000092 1.65444 10650 133 3513 118 10517 3395 0 1 1.65444
c1348_1000101 1.34993 2126 142 889 119 1984 770 0 1 1.34993
c1348_1000102 1.43936 2781 158 1088 130 2623 958 0 1 1.43936

Total number of rows: 9858

Table truncated, full table size 586 Kbytes.




Supplementary file Size Download File type/resource
GSM160781.gpr.gz 903.5 Kb (ftp)(http) GPR
Processed data included within Sample table

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