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Sample GSM195065 Query DataSets for GSM195065
Status Public on Feb 08, 2008
Title BT549
Sample type RNA
 
Channel 1
Source name BT549
Organism Homo sapiens
Characteristics tumor cell line
Growth protocol Cell lines were grown from the publicly available NCI DTP frozen stocks in RPMI-1640 supplemented with phenol red, glutamine (2 mM) and 5% fetal calf serum. To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium.
Extracted molecule polyA RNA
Extraction protocol To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium. Cells were lysed in buffer containing Protein/Rnase Degrader (Invitrogen) and messenger RNA was purified with the FastTrack 2.0 purification kit (Invitrogen).
Label Cy3
Label protocol For each comparative array hybridization, labeled cDNA was synthesized by reverse transcription from test cell mRNA in the presence of Cy5-dUTP, and from the reference mRNA with Cy3-dUTP, using the Superscript II reverse-transcription kit (Gibco-BRL).
 
Channel 2
Source name Reference Batch CRH
Organism Homo sapiens
Characteristics Tumor cell line pool
Extracted molecule polyA RNA
Extraction protocol To minimize the contribution of variations in culture conditions or cell density to differential gene expression, we grew each cell line to 80% confluence and isolated mRNA 24 hours after transfer to fresh medium. Cells were lysed in buffer containing Protein/Rnase Degrader (Invitrogen) and messenger RNA was purified with the FastTrack 2.0 purification kit (Invitrogen).
Label Cy5
Label protocol For each comparative array hybridization, labeled cDNA was synthesized by reverse transcription from test cell mRNA in the presence of Cy5-dUTP, and from the reference mRNA with Cy3-dUTP, using the Superscript II reverse-transcription kit (Gibco-BRL).
 
 
Hybridization protocol 65°C overnight in a water bath.
Scan protocol All arrays were scanned using GenePix 4000A microarray scanner (Axon Instruments, Union City, CA) and initial data analysis was carried out using GenePix Pro 3.0
Description Simple annotation: Cell-line, Pharmacogenomics
Image: http://smd.stanford.edu/MicroArray/gifs/2002-03/26854.gif
Data processing Array elements were manually flaged to exclude apparent problematic spots. All non-flagged array elements for which the fluorescent intensity in each channel was at least 300 units and the regression correlation between the red and green channels was greater than 0.6 were considered well measured and included in the study. Inclusion of a gene in correlative studies required that greater than 80% of measurements across all the cell lines in the study were present.
 
Submission date May 29, 2007
Last update date Feb 08, 2008
Contact name Douglas Ross
E-mail(s) dross@applied-genomics.com
Phone 650-697-8900
Fax 697-8900
Organization name Applied-Genomics
Street address 863 Mitten Rd #103
City Burlingame
State/province CA
ZIP/Postal code 94010
Country USA
 
Platform ID GPL3043
Series (1)
GSE7947 Gene expression patterns within cell lines are predictive of chemosensitivity

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
1 873 1389 179 172 694 1217 902 1414 180 174 723 1242 0 0 215 480 28 39 100 100 100 100 1911 1965 .57 1.754 1.718 1.684 1.777 1.398 80 415 1.86 .95 100 2240 7330 52 62 67 77 0 1229 152 1077 1.552 1251 1099 .644 1.52 .634 .604
2 600 671 182 177 418 494 617 682 184 179 435 505 0 0 117 154 28 40 100 100 100 100 912 940 .846 1.182 1.161 1.173 1.131 1.358 80 344 1.205 .93 100 2380 7330 52 62 81 91 0 594 157 437 1.046 604 447 .956 1.027 .065 .039
3 2981 2119 183 177 2798 1942 3122 2221 184 180 2939 2044 0 0 781 774 32 44 100 100 100 100 4740 4983 1.441 .694 .695 .646 .754 1.635 80 419 .646 .89 110 2530 7320 50 61 95 106 0 1875 157 1719 .614 1965 1809 1.628 .615 -.703 -.7
4 7009 7477 190 175 6819 7302 7305 7998 191 177 7115 7823 0 0 3870 4174 35 42 100 100 100 100 14121 14938 .934 1.071 1.1 1.129 1.068 1.825 120 446 1.073 .98 120 2680 7330 51 63 110 122 0 6617 155 6462 .948 7078 6923 1.055 .973 -.078 -.039
5 1024 1029 193 172 831 857 1049 1023 197 176 856 851 0 0 273 270 37 48 100 100 100 100 1688 1707 .97 1.031 .994 1.037 1.056 1.317 80 301 1.031 .95 100 2820 7330 52 62 125 135 0 911 152 758 .913 905 753 1.096 .88 -.132 -.185
6 469 602 192 171 277 431 487 621 194 175 295 450 0 0 77 131 31 42 100 100 100 100 708 745 .643 1.556 1.525 1.547 1.564 1.359 52 292 1.67 .89 90 2960 7330 52 61 139 148 0 533 151 381 1.377 550 398 .726 1.35 .461 .433
7 1255 430 197 176 1058 254 1323 422 197 178 1126 246 0 0 265 87 31 42 100 100 100 98 1312 1372 4.165 .24 .218 .235 .246 1.371 80 415 .232 .88 110 3110 7330 51 62 153 164 0 381 156 225 .212 373 218 4.707 .193 -2.235 -2.371
8 6085 9979 197 175 5888 9804 6772 11228 198 178 6575 11053 0 0 2630 4216 33 41 99 100 99 100 15692 17628 .601 1.665 1.681 1.81 1.636 1.797 120 472 1.664 .98 120 3260 7330 51 63 168 180 0 8831 155 8676 1.474 9936 9781 .679 1.488 .559 .573
9 1340 3036 200 169 1140 2867 1334 3147 201 171 1134 2978 0 0 299 690 30 42 100 100 100 100 4007 4112 .398 2.515 2.626 2.523 2.486 1.214 80 324 2.552 .97 100 3400 7330 52 62 183 193 0 2687 150 2537 2.226 2785 2635 .449 2.324 1.154 1.217
10 583 613 200 164 383 449 599 628 213 177 399 464 0 0 92 114 106 82 100 100 94 100 832 863 .853 1.172 1.163 1.168 1.209 1.339 52 245 1.151 .92 90 3550 7340 53 62 198 207 0 542 145 397 1.037 556 411 .964 1.029 .053 .041
11 2486 2564 204 164 2282 2400 2553 2713 208 178 2349 2549 0 0 1088 1124 59 103 99 99 95 98 4682 4898 .951 1.052 1.085 1.105 1.065 1.616 120 453 1.046 .98 120 3700 7330 51 63 212 224 0 2269 145 2124 .931 2401 2256 1.074 .96 -.104 -.058
12 2036 3446 196 171 1840 3275 1989 3527 200 189 1793 3356 0 0 592 1133 32 122 100 100 100 100 5115 5149 .562 1.78 1.872 1.761 1.783 1.197 52 269 1.847 .97 90 3840 7320 51 60 227 236 0 3050 151 2898 1.575 3121 2970 .635 1.656 .655 .728
13 1082 2081 197 166 885 1915 1088 2014 201 176 891 1848 0 0 494 976 31 79 96 97 93 95 2800 2739 .462 2.164 2.074 2.217 2.169 1.319 80 356 2.135 .98 100 3990 7330 52 62 242 252 0 1842 147 1695 1.915 1782 1635 .522 1.835 .937 .876
14 464 572 208 154 256 418 463 611 207 160 255 457 0 0 157 198 34 38 90 94 88 94 674 712 .612 1.633 1.792 1.669 1.642 1.422 52 242 1.479 .91 80 4140 7330 53 61 258 266 0 506 136 370 1.445 541 404 .692 1.586 .531 .665
15 6435 10181 204 159 6231 10022 6767 10589 205 160 6563 10430 0 0 1513 2487 32 35 100 100 100 100 16253 16993 .622 1.608 1.589 1.605 1.61 1.191 80 427 1.625 .98 110 4280 7330 51 62 270 281 0 9010 141 8869 1.423 9371 9230 .703 1.406 .509 .492
16 2406 2878 198 165 2208 2713 2353 2853 201 167 2155 2688 0 0 547 684 30 37 100 100 100 100 4921 4843 .814 1.229 1.247 1.228 1.189 1.217 80 365 1.226 .97 100 4430 7330 52 62 286 296 0 2547 146 2401 1.087 2525 2379 .92 1.104 .121 .143
17 436 625 197 163 239 462 438 618 199 165 241 455 0 0 88 146 30 38 98 100 98 100 701 696 .517 1.933 1.888 2.003 1.852 1.408 52 298 1.995 .91 90 4570 7330 52 61 300 309 0 553 144 409 1.711 547 403 .585 1.671 .775 .741
18 441 512 209 160 232 352 436 521 209 161 227 361 0 0 79 131 31 38 100 100 98 100 584 588 .659 1.517 1.59 1.509 1.491 1.479 52 285 1.617 .89 90 4730 7330 52 61 316 325 0 453 142 312 1.343 461 319 .745 1.407 .425 .493
19 1292 1382 218 156 1074 1226 1346 1433 219 156 1128 1277 0 0 240 269 31 37 100 100 100 100 2300 2405 .876 1.142 1.132 1.144 1.14 1.213 80 411 1.137 .97 110 4860 7330 51 62 328 339 0 1223 138 1085 1.01 1268 1130 .99 1.002 .015 .003
20 544 741 221 153 323 588 554 734 222 156 333 581 0 0 85 154 31 35 100 100 100 100 911 914 .549 1.82 1.745 1.836 1.778 1.36 52 300 1.888 .91 90 5010 7330 52 61 344 353 0 656 135 520 1.611 650 514 .621 1.544 .688 .627

Total number of rows: 43008

Table truncated, full table size 9403 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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