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Sample GSM160762 Query DataSets for GSM160762
Status Public on Aug 14, 2007
Title SP HU syn WT harvested at 030 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 30 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 0.711054 4846 107 3070 76 4739 2994 0 1 0.711054
c1348_1000012 0.437228 1807 112 1332 69 1695 1263 0 1 0.437228
c1348_1000021 -0.00723157 2272 113 2208 69 2159 2139 0 1 -0.00723157
c1348_1000022 0.559737 1798 140 1301 112 1658 1189 0 1 0.559737
c1348_1000031 0.136191 2546 117 2500 79 2429 2421 0 1 0.136191
c1348_1000032 0.154454 1532 116 1400 89 1416 1311 0 1 0.154454
c1348_1000041 0.355016 1581 114 1209 72 1467 1137 0 1 0.355016
c1348_1000042 0.288063 1305 115 1053 70 1190 983 0 1 0.288063
c1348_1000051 0.209141 635 105 533 79 530 454 0 1 0.209141
c1348_1000052 0.0328061 557 117 495 77 440 418 0 1 0.0328061
c1348_1000061 0.390668 1160 101 898 73 1059 825 0 1 0.390668
c1348_1000062 0.27858 908 112 743 88 796 655 0 1 0.27858
c1348_1000071 -0.0101344 1185 103 1135 75 1082 1060 0 1 -0.0101344
c1348_1000072 0.214125 1371 122 1146 90 1249 1056 0 1 0.214125
c1348_1000081 0.365133 1701 112 1329 79 1589 1250 0 1 0.365133
c1348_1000082 0.553852 1935 122 1356 81 1813 1275 0 1 0.553852
c1348_1000091 0.309176 1753 112 1472 116 1641 1356 0 1 0.309176
c1348_1000092 0.537048 1828 110 1283 71 1718 1212 0 1 0.537048
c1348_1000101 -0.0664274 455 113 410 71 342 339 0 1 -0.0664274
c1348_1000102 -0.0694519 522 107 458 70 415 388 0 1 -0.0694519

Total number of rows: 9858

Table truncated, full table size 580 Kbytes.




Supplementary file Size Download File type/resource
GSM160762.gpr.gz 857.3 Kb (ftp)(http) GPR
Processed data included within Sample table

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