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Sample GSM95528 Query DataSets for GSM95528
Status Public on Feb 25, 2006
Title MCF-7 (mbp 1)
Sample type RNA
 
Channel 1
Source name Free RNA
Organism Homo sapiens
Characteristics Free RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Membrane-bound RNA
Organism Homo sapiens
Characteristics Membrane-bound RNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Polysomes, membrane-bound polysomes
Image: http://smd.stanford.edu/MicroArray/gifs/2000-04/4027.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 Feb 03, 2006
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 GPL182
Series (1)
GSE4175 Genome-Scale Identification of Membrane-Associated Human mRNAs

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 1643 2247 446 479 1197 1768 522 605 68 74 1.41 112 1233 1.291 .905 29 41 44 56 0 1799 383 1415 1.182 .846 .242
2 3343 3019 619 799 2724 2220 684 867 75 73 .751 112 1017 .756 .927 29 41 59 71 0 2417 640 1777 .652 1.533 -.616
3 3715 2845 628 821 3087 2024 656 856 72 66 .644 112 1017 .649 .912 29 41 74 86 0 2277 657 1620 .525 1.905 -.93
4 689 884 536 664 153 220 585 748 25 32 1.474 112 1017 1.231 .773 29 41 89 101 0 708 532 176 1.151 .869 .203
5 826 1135 434 448 392 687 495 574 66 78 1.674 112 1017 1.179 .741 29 41 104 116 0 909 359 550 1.403 .713 .488
6 5436 5480 390 371 5046 5109 441 473 88 82 .998 112 1017 .975 .939 29 41 119 131 0 4387 297 4090 .81 1.234 -.303
7 1351 1137 372 330 979 807 395 387 48 39 .743 112 1017 .86 .901 29 41 134 146 0 910 264 646 .66 1.515 -.6
8 728 743 343 301 385 442 354 331 38 37 1.076 112 1017 1.184 .906 29 41 149 161 0 595 241 354 .919 1.088 -.122
9 8015 9726 317 294 7698 9432 330 318 82 83 1.118 112 1021 1.168 .944 28 40 164 176 0 7786 235 7550 .981 1.02 -.028
10 842 971 306 309 536 662 319 328 60 62 1.141 112 1017 1.235 .926 28 40 179 191 0 777 247 530 .989 1.011 -.016
11 897 1907 296 313 601 1594 319 343 69 75 2.638 112 1017 2.077 .857 28 40 194 206 0 1527 251 1276 2.123 .471 1.086
12 1326 2096 278 290 1048 1806 316 354 75 78 1.626 112 1017 1.559 .899 28 40 209 221 0 1678 232 1446 1.379 .725 .464
13 4212 4584 263 249 3949 4335 301 319 85 81 1.051 112 1017 1.103 .932 28 40 224 236 0 3669 199 3470 .879 1.138 -.186
14 21849 15808 242 220 21607 15588 260 242 93 94 .719 112 1017 .674 .938 28 40 239 251 0 12654 176 12478 .578 1.732 -.792
15 1309 1535 241 218 1068 1317 256 236 80 83 1.189 112 1017 1.141 .924 28 40 254 266 0 1229 175 1054 .987 1.013 -.019
16 1332 1262 244 215 1088 1047 276 235 73 74 1.009 112 1017 .85 .898 28 40 269 281 0 1010 172 838 .77 1.298 -.376
17 13967 11937 236 208 13731 11729 273 230 89 88 .815 112 1017 .794 .927 28 40 284 296 0 9555 167 9389 .684 1.462 -.548
18 778 969 226 195 552 774 261 218 72 70 1.391 112 1017 .865 .763 28 40 299 311 0 776 156 620 1.122 .891 .167
19 5270 4219 219 184 5051 4035 231 204 81 81 .722 112 1017 .77 .933 28 40 314 326 0 3377 147 3230 .639 1.564 -.645
20 2534 5870 219 183 2315 5687 237 221 83 87 2.27 112 1021 2.255 .925 28 40 329 341 0 4699 146 4552 1.966 .509 .976

Total number of rows: 24192

Table truncated, full table size 2738 Kbytes.




Supplementary data files not provided
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