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Sample GSM160748 Query DataSets for GSM160748
Status Public on Aug 14, 2007
Title SP HU syn WT harvested at 000 min Bio_2_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 0.137504 3720 118 3254 72 3602 3182 0 1 0.137504
c1348_1000012 0.00575927 1601 116 1546 75 1485 1471 0 1 0.00575927
c1348_1000021 -0.0558912 2299 121 2417 77 2178 2340 0 1 -0.0558912
c1348_1000022 0.199123 1401 125 1217 81 1276 1136 0 1 0.199123
c1348_1000031 0.0949116 2163 115 1950 68 2048 1882 0 1 0.0949116
c1348_1000032 0.107018 1399 120 1289 79 1279 1210 0 1 0.107018
c1348_1000041 0.0854247 1057 111 1016 71 946 945 0 1 0.0854247
c1348_1000042 -0.270556 805 117 919 76 688 843 0 1 -0.270556
c1348_1000051 -0.0831412 484 109 461 72 375 389 0 1 -0.0831412
c1348_1000052 -0.302226 427 114 455 71 313 384 0 1 -0.302226
c1348_1000061 0.14274 881 107 792 79 774 713 0 1 0.14274
c1348_1000062 -0.0877334 623 110 631 74 513 557 0 1 -0.0877334
c1348_1000071 0.0745054 1101 109 1006 80 992 926 0 1 0.0745054
c1348_1000072 -0.0619024 1094 114 1084 72 980 1012 0 1 -0.0619024
c1348_1000081 0.102994 1690 114 1518 73 1576 1445 0 1 0.102994
c1348_1000082 -0.200913 960 123 1075 79 837 996 0 1 -0.200913
c1348_1000091 0.111031 1418 117 1337 80 1301 1257 0 1 0.111031
c1348_1000092 0.24732 1463 113 1241 76 1350 1165 0 1 0.24732
c1348_1000101 -0.192645 336 114 320 75 222 245 0 1 -0.192645
c1348_1000102 -0.284546 349 115 361 84 234 277 0 1 -0.284546

Total number of rows: 9858

Table truncated, full table size 591 Kbytes.




Supplementary file Size Download File type/resource
GSM160748.gpr.gz 845.3 Kb (ftp)(http) GPR
Processed data included within Sample table

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