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Sample GSM71741 Query DataSets for GSM71741
Status Public on Aug 25, 2005
Title Y10 mRNP vs. Poly
Sample type RNA
 
Channel 1
Source name mRNP
Organism Saccharomyces cerevisiae
Characteristics mRNP
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Poly
Organism Saccharomyces cerevisiae
Characteristics Poly
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Stress, Nutrient limitation
Image: http://smd.stanford.edu/MicroArray/gifs//13493.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Aug 24, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL53
Series (1)
GSE3190 Response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source.

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_MEAN Uncorrected Cy3 mean pixel intensity.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2B_MEDIAN Median intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1D_MEAN The mean feature pixel intensity with the median background subtracted (channel 1).; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN The mean feature pixel intensity with the median background subtracted (channel 2).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_MEAN Mean intensities of background pixels of Cy3.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN Mean intensities of background pixels of Cy5.; Type: integer; Scale: linear_scale; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PIX_RAT2_MEDIAN Contains median of Ch2PI-CH2B/Ch1PI-CH1B where Ch1PI & Ch2PI represent single pixel intensities.; Type: float; Scale: linear_scale
TOT_SPIX Count of the number of pixels in the spot.; Type: integer; Scale: linear_scale
TOT_BPIX Number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG User defined spot flag (default 0).; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
VALUE Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1B_MEAN CH2B_MEAN PERGTBCH1I_1SD PERGTBCH2I_1SD PIX_RAT2_MEDIAN TOT_SPIX TOT_BPIX REGR CORR TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN RAT1N_MEAN VALUE
1 30904 43103 7247 9368 23657 33735 7637 9908 87 87 1.36 109 1347 0 0 209 222 222 235 0 41050 8922 32129 1.358 .736 .442
2 10613 13887 6311 8337 4302 5550 6633 8602 37 37 1.24 109 1204 0 0 209 222 240 253 0 13226 7940 5286 1.229 .814 .297
3 24105 32481 5573 7637 18532 24844 5803 7771 98 92 1.2 109 1204 0 0 209 222 258 271 0 30934 7273 23661 1.277 .783 .352
4 8669 13330 5155 7047 3514 6283 5507 7508 31 33 1.45 109 1204 0 0 209 222 276 289 0 12695 6711 5984 1.703 .587 .768
5 19318 28191 5207 7015 14111 21176 5390 7348 80 80 1.33 109 1207 0 0 209 222 294 307 0 26849 6681 20168 1.429 .7 .515
6 11136 16235 5041 6823 6095 9412 5135 6957 42 42 1.39 109 1208 0 0 209 222 313 326 -100 15462 6498 8964 1.471 .68 .556
7 4825 6555 5070 6890 -245 -335 5089 6903 3 0 .82 109 1205 0 0 209 222 331 344 -100 6243 6562 -319 null null null
8 5573 7369 5045 6874 528 495 5037 6853 3 2 1.02 109 1205 0 0 209 222 349 362 -100 7018 6547 471 .893 1.12 -.163
9 4856 6623 4759 6483 97 140 4767 6529 2 2 .89 109 1205 0 0 209 222 367 380 -100 6308 6174 133 1.375 .727 .459
10 4466 6119 4742 6672 -276 -553 4765 6640 0 0 .71 109 1195 .27 .18 209 222 385 398 -100 5828 6354 -527 null null null
11 5230 7174 4814 6750 416 424 4871 6801 3 2 1.07 109 1150 0 0 211 224 401 414 -100 6832 6429 404 .971 1.03 -.043
12 4785 6612 5117 6991 -332 -379 5134 7087 0 0 1.71 109 1177 0 0 211 224 419 432 -100 6297 6658 -361 null null null
13 4866 6916 5031 7008 -165 -92 5058 7023 1 0 .81 109 1177 0 0 211 224 437 450 -100 6587 6674 -88 null null null
14 5054 6864 4981 6876 73 -12 4947 6804 1 0 1.31 109 1177 0 0 211 224 455 468 -100 6537 6549 -11 null null null
15 4645 6668 4846 6651 -201 17 4784 6556 2 1 1.28 109 1177 0 0 211 224 473 486 -100 6350 6334 16 null null null
16 4827 6553 4770 6617 57 -64 4723 6577 1 0 .91 109 1177 0 0 211 224 491 504 -100 6241 6302 -61 null null null
17 5045 7114 4866 6817 179 297 4814 6765 1 0 1.24 109 1177 0 0 211 224 509 522 -100 6775 6492 283 1.58 .633 .66
18 4986 6925 4791 6727 195 198 4713 6633 1 1 1.09 109 1177 0 0 211 224 527 540 -100 6595 6407 189 .967 1.034 -.048
19 5086 7065 4569 6377 517 688 4521 6325 3 1 1.1 109 1177 0 0 211 224 545 558 -100 6729 6073 655 1.267 .789 .342
20 4724 6401 4498 6254 226 147 4418 6224 2 0 .82 109 1177 0 0 211 224 563 576 -100 6096 5956 140 .619 1.614 -.691

Total number of rows: 8832

Table truncated, full table size 968 Kbytes.




Supplementary data files not provided
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