NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM28844 Query DataSets for GSM28844
Status Public on Jun 13, 2005
Title cus2D_3
Sample type RNA
 
Channel 1
Source name BY4741 (cus2D) @ 26 deg
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
Channel 2
Source name BY4741 (wt) @ 26 deg
Organism Saccharomyces cerevisiae
Extracted molecule total RNA
 
 
Description Reference and mutant strains grown at 26oC to an OD of 0.5-0.6 . RNA extracted.
Empty cells (no data) are represented by the value -10000
 
Submission date Aug 12, 2004
Last update date Jun 13, 2005
Contact name Todd A Burckin
E-mail(s) burckin@biology.ucsc.edu
Phone 831 459-5245
Fax 831 459-3139
Organization name University of California Santa Cruz
Department Molecular, Cell, & Developmental Biology
Lab Hartzog Lab
Street address 1156 High Street
City Santa Cruz
State/province CA
ZIP/Postal code 95062
Country USA
 
Platform ID GPL1408
Series (1)
GSE1684 Exploring functional relationships between components of the gene expression machinery

Data table header descriptions
ID_REF
X X-coordinate of spot
Y Y-coordinate of spot
Dia. spot diameter in microns
F635 Median Channel 2 (Cy5/635) median pixel intensity - feature
F635 Mean Channel 2 (Cy5/635) mean pixel intensity - feature
F635 SD Channel 2 (Cy5/635) standard deviation of pixel intensities - feature
B635 Median Channel 2 (Cy5/635) median background intensity
B635 Mean Channel 2 (Cy5/635) mean background intensity
B635 SD Channel 2 (Cy5/635) standard deviation of background
% > B635+1SD Channel 2 (Cy5/635) percent of pixels 1 StDev above background
% > B635+2SD Channel 2 (Cy5/635) percent of pixels 2 StDevs above background
F635 % Sat. Channel 2 (Cy5/635) percent of pixels saturated
F532 Median Channel 1 (Cy3/532) median pixel intensity - feature
F532 Mean Channel 1 (Cy3/532) mean pixel intensity - feature
F532 SD Channel 1 (Cy3/532) standard deviation of pixel intensities - feature
B532 Median Channel 1 (Cy3/532) median background intensity
B532 Mean Channel 1 (Cy3/532) mean background intensity
B532 SD Channel 1 (Cy3/532) standard deviation of background
% > B532+1SD Channel 1 (Cy3/532) percent of pixels 1 StDev above background
% > B532+2SD Channel 1 (Cy3/532) percent of pixels 2 StDevs above background
F532 % Sat. Channel 1 (Cy3/532) percent of pixels saturated
F3 Median n/a
F3 Mean n/a
F3 SD n/a
B3 Median n/a
B3 Mean n/a
B3 SD n/a
% > B3+1SD n/a
% > B3+2SD n/a
F3 % Sat. n/a
F4 Median n/a
F4 Mean n/a
F4 SD n/a
B4 Median n/a
B4 Mean n/a
B4 SD n/a
% > B4+1SD
% > B4+2SD n/a
F4 % Sat. n/a
Ratio of Medians (635/532) Ratio of medians (Ch2/Ch1)
Ratio of Means (635/532) Ratio of means (Ch2/Ch1)
Median of Ratios (635/532) Median of ratios
Mean of Ratios (635/532) Mean of ratios
Ratios SD (635/532) Ratio standard deviation
Rgn Ratio (635/532) Regression ratio
Rgn R? (635/532) Regression square ratio
Ratio of Medians (Ratio/2) n/a
Ratio of Means (Ratio/2) n/a
Median of Ratios (Ratio/2) n/a
Mean of Ratios (Ratio/2) n/a
Ratios SD (Ratio/2) n/a
Rgn Ratio (Ratio/2) n/a
Rgn R? (Ratio/2) n/a
Ratio of Medians (Ratio/3) n/a
Ratio of Means (Ratio/3) n/a
Median of Ratios (Ratio/3) n/a
Mean of Ratios (Ratio/3) n/a
Ratios SD (Ratio/3) n/a
Rgn Ratio (Ratio/3) n/a
Rgn R? (Ratio/3) n/a
F Pixels Number of feature pixels
B Pixels Number of background pixels
Sum of Medians Sum of medians
Sum of Means Sum of means
VALUE Log ratio (635/532) (base 2)
Log Ratio (Ratio/2) n/a
Log Ratio (Ratio/3) n/a
F635 Median - B635 Channel 2 (Cy5/635) background subtracted median feature intensity
F532 Median - B532 Channel 1 (Cy3/532) background subtracted median feature intensity
F3 Median - B3 n/a
F4 Median - B4 n/a
F635 Mean - B635 Channel 2 (Cy5/635) background subtracted mean feature intensity
F532 Mean - B532 Channel 1 (Cy3/532) background subtracted mean feature intensity
F3 Mean - B3
F4 Mean - B4
Flags User defined flag (default=0)
Normalize n/a

Data table
ID_REF X Y Dia. F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD % > B532+1SD % > B532+2SD F532 % Sat. F3 Median F3 Mean F3 SD B3 Median B3 Mean B3 SD % > B3+1SD % > B3+2SD F3 % Sat. F4 Median F4 Mean F4 SD B4 Median B4 Mean B4 SD % > B4+1SD % > B4+2SD F4 % Sat. Ratio of Medians (635/532) Ratio of Means (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R? (635/532) Ratio of Medians (Ratio/2) Ratio of Means (Ratio/2) Median of Ratios (Ratio/2) Mean of Ratios (Ratio/2) Ratios SD (Ratio/2) Rgn Ratio (Ratio/2) Rgn R? (Ratio/2) Ratio of Medians (Ratio/3) Ratio of Means (Ratio/3) Median of Ratios (Ratio/3) Mean of Ratios (Ratio/3) Ratios SD (Ratio/3) Rgn Ratio (Ratio/3) Rgn R? (Ratio/3) F Pixels B Pixels Sum of Medians Sum of Means VALUE Log Ratio (Ratio/2) Log Ratio (Ratio/3) F635 Median - B635 F532 Median - B532 F3 Median - B3 F4 Median - B4 F635 Mean - B635 F532 Mean - B532 F3 Mean - B3 F4 Mean - B4 Flags Normalize
1 1540 25320 110 42 50 30 37 38 6 46 23 0 1317 1352 670 30 61 176 93 88 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.004 0.01 0.093 0.087 4.87 0.004 0.012 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 467 1292 1335 -8.008 -10000 -10000 5 1287 0 0 13 1322 0 0 0 0
2 1790 25320 150 38 59 62 36 37 6 30 19 0 31 36 15 29 44 124 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 3.286 1.733 1.692 2.778 4.613 0.641 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 965 4 30 0 -10000 -10000 2 2 0 0 23 7 0 0 -50 0
3 1950 25330 120 3022 2725 1003 35 36 11 100 100 0 2222 1973 856 28 29 4 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.361 1.383 1.35 1.552 1.613 1.346 0.954 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 659 5181 4635 0.445 -10000 -10000 2987 2194 0 0 2690 1945 0 0 0 0
4 2230 25320 150 37 41 26 36 38 25 2 1 0 30 33 10 29 30 18 7 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1.25 1.414 1.494 3.376 4.521 0.686 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 1036 2 9 0 -10000 -10000 1 1 0 0 5 4 0 0 -50 0
5 2340 25340 110 87 89 19 37 38 6 100 100 0 77 79 17 30 30 4 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.064 1.061 0.98 1.079 1.6 1.531 0.506 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 453 97 101 0.089 -10000 -10000 50 47 0 0 52 49 0 0 0 0
6 2550 25350 100 55 60 21 36 37 8 82 57 0 46 50 15 29 30 5 93 76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.118 1.143 1.143 1.078 1.787 1.847 0.615 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 536 36 45 0.16 -10000 -10000 19 17 0 0 24 21 0 0 0 0
7 2770 25360 110 55 65 29 36 37 8 86 60 0 46 55 22 30 31 5 93 73 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.188 1.16 1.14 1.162 1.953 1.306 0.653 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 539 35 54 0.248 -10000 -10000 19 16 0 0 29 25 0 0 0 0
8 2950 25350 120 83 90 26 37 37 6 100 100 0 74 81 30 30 30 5 100 98 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.045 1.039 1.012 1.089 1.735 0.985 0.724 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 642 90 104 0.064 -10000 -10000 46 44 0 0 53 51 0 0 0 0
9 3140 25350 110 140 149 42 36 37 9 100 100 0 124 128 29 29 30 4 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.095 1.141 1.065 1.127 1.448 1.265 0.721 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 574 199 212 0.131 -10000 -10000 104 95 0 0 113 99 0 0 0 0
10 3360 25360 120 4974 4977 2216 36 41 41 100 100 0 3902 4003 1931 29 32 27 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.275 1.243 1.272 1.348 1.425 1.227 0.94 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 698 8811 8915 0.35 -10000 -10000 4938 3873 0 0 4941 3974 0 0 0 0
11 3590 25340 150 38 73 87 35 38 35 18 15 0 29 47 44 28 31 23 18 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 2 2 1.982 2.42 1.767 0.894 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 932 4 57 1.585 -10000 -10000 3 1 0 0 38 19 0 0 -50 0
12 3770 25360 120 234 246 89 34 35 9 99 99 0 222 233 106 28 30 23 97 93 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.031 1.034 1.049 1.113 1.53 0.982 0.893 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 596 394 417 0.044 -10000 -10000 200 194 0 0 212 205 0 0 0 0
13 3970 25370 120 78 79 16 34 35 9 97 95 0 62 64 16 28 30 21 84 25 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.294 1.25 1.281 1.305 1.497 1.217 0.76 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 691 78 81 0.372 -10000 -10000 44 34 0 0 45 36 0 0 0 0
14 4230 25350 150 35 60 69 35 36 28 13 12 0 29 38 24 29 30 22 13 10 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2.778 2.127 1.75 2.292 1.785 0.777 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 961 0 34 -10000 -10000 0 0 0 0 25 9 0 0 -50 0
15 4370 25380 120 160 159 48 34 36 35 95 87 0 132 131 47 28 30 28 91 84 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.212 1.214 1.121 1.314 1.75 1.207 0.842 0 0 0 0 0 0 0 0 0 0 0 0 0 0 120 592 230 228 0.277 -10000 -10000 126 104 0 0 125 103 0 0 0 0
16 4600 25380 90 48 62 43 34 35 5 78 59 0 37 41 13 28 28 3 84 69 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.556 2.154 2.143 1.74 2.67 3.286 0.622 0 0 0 0 0 0 0 0 0 0 0 0 0 0 52 420 23 41 0.637 -10000 -10000 14 9 0 0 28 13 0 0 -50 0
17 4830 25360 150 35 38 13 34 43 180 0 0 0 29 31 7 28 34 117 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1.333 1.472 1.518 2.47 2.575 0.201 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 978 2 7 0 -10000 -10000 1 1 0 0 4 3 0 0 -50 0
18 5030 25370 150 37 40 9 35 45 189 0 0 0 32 33 6 28 35 123 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.5 1 1.375 1.196 2.829 1.649 0.728 0 0 0 0 0 0 0 0 0 0 0 0 0 0 156 871 6 10 -1 -10000 -10000 2 4 0 0 5 5 0 0 -50 0
19 5200 25390 100 47 51 14 35 35 6 83 46 0 40 41 8 29 29 4 86 70 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.091 1.333 1.091 1.248 2.492 1.836 0.351 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 417 23 28 0.126 -10000 -10000 12 11 0 0 16 12 0 0 -50 0
20 5380 25380 100 42 44 9 34 35 11 32 10 0 36 36 6 28 29 5 67 35 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1.25 1.309 1.228 2.71 2.022 0.17 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 504 16 18 0 -10000 -10000 8 8 0 0 10 8 0 0 -50 0

Total number of rows: 6400

Table truncated, full table size 1548 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap