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Sample GSM719379 Query DataSets for GSM719379
Status Public on Jan 06, 2012
Title Hs578t sample A
Sample type RNA
 
Channel 1
Source name stratagene human reference plus doping controls.
Organism Homo sapiens
Characteristics reference: stratagene human reference plus doping controls.
Extracted molecule total RNA
Extraction protocol MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions
Label Cy3
Label protocol StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene
Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH1; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)
 
Channel 2
Source name Hs578t sample A plus doping controls.
Organism Homo sapiens
Characteristics cells: Hs578t sample A plus doping controls.
Growth protocol osteoblast co-culture; Human mammary epithelial cells (HMEC) (Cambrex Bio Science Walkersville, Walkersville, MD) were expanded in mammary epithelial basal medium that was supplemented with bovine pituitary extract, human EGF, insulin and antibiotics (Clonetics, Cambrex Bio Science Walkersville, Walkersville, MD). MCF-7, T47D, MDA-MB231, SKBR-3, Hs578T, (ATCC, Atlanta, GA) were propagated in DMEM with 4.5% glucose (Gibco, Grand Island, NY) that was supplemented with 10% FBS (HyClone, Logan, UT), glutamine, 100 U/ml penicillin and 100 ??g/ml streptomycin (Gibco, Grand Island, NY). Normal human Osteoblasts (NHOST) (Lonza Walkersville, Walkersville, MD) were expanded in Clonetics Osteoblast Basal Medium (OBM???) (Lonza Walkersville, Walkersville, MD) supplemented with osteoblast growth medium (OGM TM) SingleQuots?? (Lonza Walkersville, Walkersville, MD) with 10 % FBS. For the co-culture experiments, the cells were cultivated for 48 hours at equal density of 30???000 cells/cm2 (15???000 tumor cells /cm2 and 15???000 normal human Osteoblast cells /cm2) in Clonetics Osteoblast Basal Medium (OBM???) supplemented with 0.2% FBS without any further additives. This medium served as a good universal media for all the cells in the study
Extracted molecule total RNA
Extraction protocol RNeasy; Total RNA was isolated using the RNeasy mini kit (QIAGEN), according to the manufacturer's instructions.; Protocol Type = Extract preparation; Performer: Michal,,Rajski
MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions
Label Cy5
Label protocol Ambion MessageAmpII Amino Allyl and Cy Dye Coupling for Oligo Arrays CH2; RNA was processed using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the protocol of Kate Rubins/Brown Lab - 04/14/2006 (update 05/25/2006)
 
 
Hybridization protocol not provided
Scan protocol Scanner Model: GenePix 4100A 01
Description Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2010-01/86214.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date May 03, 2011
Last update date Jan 06, 2012
Contact name Michal Rajski
E-mail(s) [email protected]
Organization name University of Zurich
Department Institute of Physiology
Lab 23K86
Street address Winterthurerstrasse 190
City Zurich
ZIP/Postal code CH - 8057
Country Switzerland
 
Platform ID GPL13482
Series (2)
GSE29031 Normal human osteoblasts and Hs578t mono and coculture
GSE29036 Global gene expression analysis of heterotypic interactions between cancer cells and osteoblasts in vitro

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; 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
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total 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
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; 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 The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; 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
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; 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
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN 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
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 2648 3006 223 180 2425 2826 2708 3099 230 184 2485 2919 0 0 1091 1189 53 47 97 100 97 100 5251 5404 .858 1.165 1.175 1.233 1.185 1.696 80 440 1.157 .97 100 1770 5930 33 43 70 80 0 2485 149 2336 .963 2562 2413 1.038 .971 -.054 -.042
2 4248 5183 230 183 4018 5000 4256 5159 238 187 4026 4976 0 0 1198 1561 52 47 100 100 100 100 9018 9002 .804 1.244 1.236 1.224 1.258 1.366 80 252 1.261 .97 100 1930 5930 33 43 86 96 0 4285 151 4134 1.029 4265 4114 .972 1.022 .041 .031
3 17140 21910 229 180 16911 21730 18464 23086 234 187 18235 22906 0 0 4975 5587 51 45 100 100 100 100 38641 41141 .778 1.285 1.256 1.366 1.265 1.639 80 315 1.252 .97 110 2070 5920 31 42 99 110 0 18114 149 17965 1.062 19086 18937 .941 1.039 .087 .055
4 4892 6074 228 180 4664 5894 4863 5936 234 187 4635 5756 0 0 1354 1430 48 47 100 100 100 100 10558 10391 .791 1.264 1.242 1.293 1.276 1.268 80 270 1.243 .98 100 2220 5920 32 42 115 125 0 5022 149 4873 1.045 4908 4759 .957 1.027 .063 .038
5 1481 1137 229 183 1252 954 1492 1168 235 192 1263 985 0 0 321 259 51 61 100 100 100 98 2206 2248 1.312 .762 .78 .742 .802 1.423 80 232 .747 .95 100 2360 5930 33 43 129 139 0 940 151 789 .63 966 814 1.587 .645 -.667 -.633
6 26115 47604 243 206 25872 47398 25859 47151 257 281 25616 46945 0 0 5258 7781 85 433 100 100 100 100 73270 72561 .546 1.832 1.833 1.847 1.831 1.129 52 220 1.85 .98 90 2500 5930 33 42 143 152 0 39356 170 39186 1.515 38982 38812 .66 1.515 .599 .599
7 597 516 233 193 364 323 611 517 242 255 378 324 0 0 98 79 80 396 100 12 98 0 687 702 1.127 .887 .857 .894 .843 1.459 80 264 1.671 .58 100 2660 5930 33 43 159 169 0 427 160 267 .734 427 268 1.363 .709 -.447 -.497
8 18027 23344 244 193 17783 23151 17708 23338 250 237 17464 23145 0 0 1761 2046 68 280 100 100 100 100 40934 40609 .768 1.302 1.325 1.303 1.31 1.095 52 214 1.29 .99 90 2790 5930 33 42 172 181 0 19300 160 19140 1.076 19295 19135 .929 1.096 .106 .132
9 412 329 242 187 170 142 410 332 249 218 168 145 0 0 67 59 62 231 96 7 72 0 312 313 1.197 .835 .863 .81 .735 1.91 80 321 3.742 .35 100 2950 5930 33 43 188 198 0 272 155 117 .691 274 120 1.448 .714 -.534 -.487
10 398 339 257 207 141 132 386 343 264 215 129 136 0 0 64 75 67 64 90 78 46 51 273 265 1.068 .936 1.054 1.023 .899 2.368 52 236 .957 .6 90 3100 5930 33 42 203 212 0 280 171 109 .774 284 112 1.292 .872 -.37 -.198
11 1837 2786 254 209 1583 2577 1819 2696 265 229 1565 2487 0 0 229 368 71 102 100 100 100 100 4160 4052 .614 1.628 1.589 1.629 1.614 1.154 52 250 1.651 .98 90 3230 5930 33 42 216 225 0 2303 173 2131 1.346 2229 2056 .743 1.314 .429 .394
12 420 406 229 188 191 218 419 410 230 200 190 222 0 0 75 70 56 93 100 96 84 71 409 412 .876 1.141 1.168 1.174 1.176 1.702 52 259 1.107 .71 90 3390 5930 33 42 232 241 0 336 155 180 .944 339 184 1.06 .966 -.084 -.05
13 802 990 223 191 579 799 819 988 233 193 596 797 0 0 184 235 103 51 98 98 96 98 1378 1393 .725 1.38 1.337 1.392 1.382 1.571 80 359 1.357 .93 100 3530 5920 32 42 246 256 0 818 158 661 1.141 817 659 .877 1.106 .19 .145
14 713 782 221 182 492 600 704 768 226 185 483 586 0 0 119 105 53 46 100 100 100 100 1092 1069 .82 1.22 1.213 1.242 1.276 1.302 52 241 1.205 .92 90 3680 5930 33 42 261 270 0 647 150 496 1.008 635 484 .992 1.003 .012 .004
15 384 287 218 178 166 109 391 287 223 186 173 109 0 0 74 58 50 45 93 88 83 62 275 282 1.523 .657 .63 .638 .638 2.177 80 298 .584 .53 100 3830 5930 33 43 276 286 0 237 147 90 .543 237 90 1.842 .521 -.881 -.941
16 2906 4438 225 186 2681 4252 2831 4378 229 191 2606 4192 0 0 412 604 62 46 100 100 100 100 6933 6798 .631 1.586 1.609 1.588 1.605 1.107 52 258 1.605 .98 90 3970 5920 32 41 290 299 0 3669 154 3515 1.311 3620 3466 .763 1.33 .391 .411
17 408 435 231 194 177 241 402 436 236 196 171 242 0 0 75 92 59 51 96 97 80 97 418 413 .734 1.362 1.415 1.359 1.381 1.608 80 374 1.362 .72 100 4120 5930 33 43 305 315 0 360 160 199 1.126 360 200 .888 1.17 .171 .227
18 366 300 231 186 135 114 375 302 235 193 144 116 0 0 66 43 52 50 92 94 63 65 249 260 1.184 .844 .806 .812 .871 2.589 52 270 .75 .53 90 4270 5930 33 42 320 329 0 248 154 94 .698 250 96 1.432 .666 -.518 -.586
19 356 299 221 182 135 117 356 289 223 186 135 107 0 0 66 61 48 42 90 90 69 69 252 242 1.154 .867 .793 .85 .771 2.315 52 247 .846 .52 90 4410 5940 34 43 334 343 0 247 150 97 .717 239 88 1.396 .655 -.481 -.61
20 319 282 218 182 101 100 315 275 220 182 97 93 0 0 76 70 52 41 77 78 47 52 201 190 1.01 .99 .959 .935 .854 2.979 80 296 .91 .41 100 4560 5930 33 43 349 359 0 233 150 83 .819 227 77 1.222 .793 -.289 -.335

Total number of rows: 49152

Table truncated, full table size 10697 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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