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Sample GSM160751 Query DataSets for GSM160751
Status Public on Aug 14, 2007
Title SP HU syn WT harvested at 010 min Bio_1
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 10 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 -0.184425 6464 132 7253 103 6332 7150 0 1 -0.184425
c1348_1000012 -0.54372 2312 141 3545 104 2171 3441 0 1 -0.54372
c1348_1000021 -0.790859 3450 140 5942 103 3310 5839 0 1 -0.790859
c1348_1000022 -1.23447 1179 172 2597 137 1007 2460 0 1 -1.23447
c1348_1000031 -0.971431 2947 143 5499 106 2804 5393 0 1 -0.971431
c1348_1000032 -1.04097 1461 146 2875 117 1315 2758 0 1 -1.04097
c1348_1000041 -0.558517 1658 155 2352 111 1503 2241 0 1 -0.558517
c1348_1000042 -0.471929 1616 170 2159 111 1446 2048 0 1 -0.471929
c1348_1000051 -0.471929 671 127 869 105 544 764 0 1 -0.471929
c1348_1000052 -0.614845 690 129 900 100 561 800 0 1 -0.614845
c1348_1000061 -0.475936 1239 148 1688 108 1091 1580 0 1 -0.475936
c1348_1000062 -0.590745 938 172 1364 115 766 1249 0 1 -0.590745
c1348_1000071 -1.20423 1105 154 2292 118 951 2174 0 1 -1.20423
c1348_1000072 -1.1047 1191 166 2443 126 1025 2317 0 1 -1.1047
c1348_1000081 -0.409278 2153 125 3034 108 2028 2926 0 1 -0.409278
c1348_1000082 -0.358454 2236 176 2840 118 2060 2722 0 1 -0.358454
c1348_1000091 -0.239566 2529 161 3001 126 2368 2875 0 1 -0.239566
c1348_1000092 -0.226004 2362 160 2683 114 2202 2569 0 1 -0.226004
c1348_1000101 -0.852042 460 161 659 108 299 551 0 1 -0.852042
c1348_1000102 -0.913216 477 94 824 63 383 761 0 1 -0.913216

Total number of rows: 9858

Table truncated, full table size 609 Kbytes.




Supplementary file Size Download File type/resource
GSM160751.gpr.gz 869.1 Kb (ftp)(http) GPR
Processed data included within Sample table

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