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Sample GSM30578 Query DataSets for GSM30578
Status Public on Nov 05, 2004
Title tub1D_SHI experiment1
Sample type RNA
 
Channel 1
Source name Pool resulting from ura3D::URA3 transformation
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
Channel 2
Source name Pool resulting from tub1D::URA3 transformation
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 ura3D::URA3 (as target source1) or a tub1D::URA3 (as target source2) cassette.
The two Pools of diploid YKOs were harvested after incubation at 30 degree for 2 days on SC-Ura medium.
Genomic DNA samples were prepared from these two 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 Hopkins-TagArray.
Fluorescent array images were collected for both Cy5 and Cy3 with a GenePix4000B microarray scanner.
The image data was annalyzed with a GenePix5.1 program.
Keywords = tub1D, SHI, heterozygotes, YKO
 
Submission date Sep 13, 2004
Last update date May 27, 2005
Contact name Xuewen Pan
E-mail(s) [email protected]
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 GPL1444
Series (2)
GSE1760 TUB1 synthetic haploinsufficiency
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 8254 86 8642 290 8168 8352 -0.2175913 0 0.86
2 4535 92 6922 300 4443 6622 -0.7612133 0 0.59
3 5566 90 3916 300 5476 3616 0.4114263 0 1.33
4 9314 91 5788 287 9223 5501 0.5558163 0 1.47
5 160 93 597 330 67 267 -2.1844253 -50 0.22
6 714 95 1220 305 619 915 -0.7612133 0 0.59
7 4052 84 4215 291 3968 3924 -0.1681233 0 0.89
8 10388 91 9696 296 10297 9400 -0.0588943 0 0.96
9 7036 85 6403 299 6951 6104 0.0000003 0 1.00
10 3807 89 1967 298 3718 1669 0.9634743 0 1.95
11 508 83 934 289 425 645 -0.7858753 0 0.58
12 1519 91 2271 289 1428 1982 -0.6665763 0 0.63
13 18622 89 16128 304 18533 15824 0.0426443 0 1.03
14 13801 94 18156 278 13707 17878 -0.5777673 0 0.67
15 9847 78 6778 272 9769 6506 0.4005383 0 1.32
16 123 89 469 288 34 181 -2.6438563 -50 0.16
17 6711 85 5983 288 6626 5695 0.0285693 0 1.02
18 2614 93 2066 288 2521 1778 0.3103403 0 1.24
19 11939 91 8021 289 11848 7732 0.4222333 0 1.34
20 16689 93 7147 293 16596 6854 1.0840643 0 2.12

Total number of rows: 22575

Table truncated, full table size 1071 Kbytes.




Supplementary file Size Download File type/resource
GSM30578_cy3.tif.gz 15.8 Mb (ftp)(http) TIFF
GSM30578_cy5.tif.gz 14.6 Mb (ftp)(http) TIFF

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