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Sample GSM30569 Query DataSets for GSM30569
Status Public on Nov 05, 2004
Title sgs1D dSLAM UpTag experiment2
Sample type RNA
 
Channel 1
Source name Pool of haploid single YKOs
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
Channel 2
Source name Pool of haploid double YKOs
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
 
Description A pool of 5,896 haploid-convertible heterozygous diploid yeast knockout (YKO) strains were transformed with a sgs1D::URA3 cassette.
The resultant diploid double YKO pool was sporulated and the spores were spread on MM with 0.1% 5-FOA (as target source1) and MM-Ura (as target source2).
Pools of haploid YKOs were harvested after incubation at 30 degree for 2 days.
Genomic DNA samples were prepared from these two haploid pools and used as the templates for PCR amplification of the TAGs identifying the YKOs with a pair of primers universal for either Uptags or Downtags.
The PCR products from sample1 were labeled with Cy5 and those from sample2 with Cy3.
The Cy5- and Cy3-labeled Uptags and Downtags were mixed together and hybridized to a Rosetta_UpTag.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with the Imagene 5.0 and Genesight 3.1 programs from Biodiscovery.
Keywords = sgs1D, dSLAM, heterozygotes, YKO
 
Submission date Sep 13, 2004
Last update date May 27, 2005
Contact name Xuewen Pan
E-mail(s) xpan2@jhmi.edu
Phone 410-955-2477
Organization name Johns Hopkins University School of Medicine
Department Department of Molecular Biology and Genetics
Lab Boeke Lab
Street address 733 N. Broadway, Room 331
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platform ID GPL1446
Series (2)
GSE1757 SGS1 synthetic lethality
GSE1838 dSLAM

Data table header descriptions
ID_REF Serial identifier for probe
F635_Median Cy5 (F635) median fluorescence intensity
B635_Median Cy5 (F635) background median fluorescence intensity
F532_Median Cy3 (F532) median fluorescence intensity
B532_Median Cy3 (F532) background median fluorescence intensity
F635-B635_Median Background substracted Cy5 (F635) median fluorescence intensity
F532-B532_Median Background substracted Cy3 (F532) median fluorescence intensity
VALUE log ratio (log2 of PRE_VALUE)
Flags
PRE_VALUE Normalized ratio defined by F635-B635_Median/F532-B532_Median

Data table
ID_REF F635_Median B635_Median F532_Median B532_Median F635-B635_Median F532-B532_Median VALUE Flags PRE_VALUE
1 127.5 122 334 261.5 5.5 72.5 -3.6438563 -50 0.08
2 153 121 331 241 32 90 -1.3584543 -50 0.39
3 110 110 298 250 0 48 -50 0.00
4 1588 117 1103 273 1471 830 0.9634743 0 1.95
5 121 112 306 276 9 30 -1.5994623 -50 0.33
6 300.5 112.5 565 277 188 288 -0.4739313 -50 0.72
7 456 117 558 263.5 339 294.5 0.3448283 -50 1.27
8 975 117 1798 256 858 1542 -0.7131193 0 0.61
9 509 104 737.5 259.5 405 478 -0.1046973 0 0.93
10 195 108 455 266 87 189 -0.9714313 -50 0.51
11 328 112 297 261 216 36 2.7246503 -50 6.61
12 376 110.5 701.5 276 265.5 425.5 -0.5353323 -50 0.69
13 4835 112 3813 261.5 4723 3551.5 0.5558163 0 1.47
14 4562 111 4132.5 284.5 4451 3848 0.3448283 0 1.27
15 128 105 348 252 23 96 -1.9434163 -50 0.26
16 113 91 335.5 252 22 83.5 -1.7858753 -50 0.29
17 3031 109 2354.5 288.5 2922 2066 0.6415463 0 1.56
18 3107 107 2077 276 3000 1801 0.8797063 0 1.84
19 1795.5 95 2292 250 1700.5 2042 -0.1202943 0 0.92
20 2622.5 110 1828 253 2512.5 1575 0.8155753 0 1.76

Total number of rows: 18792

Table truncated, full table size 917 Kbytes.




Supplementary file Size Download File type/resource
GSM30569_cy3.tif.gz 13.7 Mb (ftp)(http) TIFF
GSM30569_cy5.tif.gz 12.9 Mb (ftp)(http) TIFF

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