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Sample GSM195074 Query DataSets for GSM195074
Status Public on Feb 08, 2008
Title CCRF-CEM
Sample type RNA
 
Channel 1
Source name CCRF-CEM
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/2002-03/26803.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
1 835 1168 165 171 670 997 920 1251 168 176 755 1080 0 0 549 598 33 42 83 92 80 90 1667 1835 .672 1.488 1.43 1.579 1.442 2.24 80 456 1.358 .89 110 1840 8010 51 62 42 53 0 1343 197 1146 1.71 1438 1241 .585 1.644 .774 .717
2 822 576 173 172 649 404 966 651 174 177 793 479 0 0 415 259 34 47 86 85 82 82 1053 1272 1.606 .622 .604 .688 .632 2.027 80 334 .592 .89 100 1980 8010 52 62 57 67 0 662 198 464 .716 748 551 1.398 .694 -.483 -.526
3 4987 791 175 172 4812 619 5857 796 176 176 5682 624 0 0 2979 420 35 49 97 91 97 85 5431 6306 7.774 .129 .11 .139 .126 2.361 80 409 .113 .86 110 2130 8010 51 62 71 82 0 909 198 711 .148 915 717 6.763 .126 -2.758 -2.986
4 9689 7604 180 184 9509 7420 9714 7139 181 192 9534 6955 0 0 6119 4859 36 50 100 100 100 100 16929 16489 1.282 .78 .729 .899 .746 2.029 80 407 .77 .94 110 2270 8000 50 61 85 96 0 8740 211 8529 .897 8206 7994 1.115 .838 -.157 -.254
5 1491 652 188 190 1303 462 1528 667 196 203 1340 477 0 0 898 269 65 74 88 91 87 85 1765 1817 2.82 .355 .356 .381 .372 1.616 80 414 .307 .89 100 2420 8010 52 62 101 111 0 749 218 531 .408 767 548 2.454 .409 -1.295 -1.289
6 462 586 187 198 275 388 437 590 202 219 250 392 0 0 199 230 79 94 84 87 71 84 663 642 .709 1.411 1.568 1.431 1.327 1.669 32 198 1.205 .83 70 2580 8000 52 59 118 125 0 674 228 446 1.622 678 451 .617 1.802 .698 .85
7 2175 418 178 196 1997 222 2644 452 177 202 2466 256 0 0 1170 186 33 48 88 80 86 77 2219 2722 8.995 .111 .104 .147 .125 2.303 80 372 .112 .86 100 2710 8010 52 62 130 140 0 480 225 255 .128 520 294 7.826 .119 -2.968 -3.067
8 9943 10246 177 201 9766 10045 11746 11404 177 205 11569 11203 0 0 5689 5129 34 47 97 100 97 100 19811 22772 .972 1.029 .968 1.314 .986 2.466 80 373 .97 .94 110 2860 8010 51 62 144 155 0 11777 231 11546 1.182 13108 12877 .846 1.113 .242 .155
9 1426 1281 179 199 1247 1082 1382 1288 186 206 1203 1089 0 0 881 654 54 58 87 97 85 95 2329 2292 1.152 .868 .905 .917 .831 2.168 80 337 .805 .93 100 3000 8010 52 62 159 169 0 1472 229 1244 .997 1480 1252 1.003 1.041 -.004 .057
10 618 539 178 187 440 352 647 558 184 194 469 371 0 0 313 241 56 60 76 82 76 76 792 840 1.25 .8 .791 .844 .815 1.84 52 225 .687 .86 80 3140 8000 52 60 174 182 0 620 215 405 .92 641 426 1.088 .909 -.121 -.137
11 3608 3108 175 180 3433 2928 3695 3086 176 186 3520 2906 0 0 1519 1230 37 45 100 100 98 100 6361 6426 1.172 .853 .826 .928 .863 1.868 80 349 .835 .95 100 3290 8000 51 61 188 198 0 3572 207 3366 .98 3547 3340 1.02 .949 -.029 -.076
12 1834 2188 171 180 1663 2008 1582 1932 175 187 1411 1752 0 0 1329 1531 35 48 92 94 92 92 3671 3163 .828 1.207 1.242 1.095 1.117 1.8 52 276 1.182 .94 90 3420 8000 51 60 201 210 0 2515 207 2308 1.388 2221 2014 .721 1.427 .473 .513
13 1229 1241 173 195 1056 1046 1128 1242 179 198 955 1047 0 0 873 763 54 50 85 88 78 87 2102 2002 1.01 .991 1.096 1.055 .985 2.98 80 379 .936 .91 100 3580 8010 52 62 217 227 0 1426 224 1202 1.139 1428 1203 .878 1.26 .187 .334
14 444 615 176 194 268 421 381 561 177 195 205 367 0 0 158 185 51 74 91 100 83 100 689 572 .637 1.571 1.79 1.788 1.802 1.817 12 94 1.298 .88 50 3710 7990 52 57 232 237 0 707 223 484 1.806 645 422 .554 2.058 .852 1.041
15 12645 11424 178 199 12467 11225 14911 13427 186 211 14733 13228 0 0 8140 6523 71 80 97 98 91 97 23692 27961 1.111 .9 .898 1.245 .91 2.669 80 508 .868 .95 110 3870 8000 50 61 245 256 0 13131 229 12902 1.035 15433 15205 .966 1.032 .05 .045
16 2609 1749 169 206 2440 1543 2975 1733 172 217 2806 1527 0 0 1700 1074 36 62 82 88 80 84 3983 4333 1.581 .632 .544 .65 .616 1.615 52 265 .567 .93 80 4010 8000 52 60 261 269 0 2010 237 1774 .727 1992 1755 1.376 .626 -.46 -.677
17 527 462 169 207 358 255 581 448 178 219 412 241 0 0 275 141 58 70 78 93 78 75 613 653 1.404 .712 .585 .656 .636 2.068 32 220 .597 .71 70 4160 7990 51 58 276 283 0 531 238 293 .819 515 277 1.221 .672 -.289 -.573
18 435 440 172 192 263 248 417 460 174 198 245 268 0 0 149 146 32 44 92 84 90 84 511 513 1.06 .943 1.094 .941 .998 1.942 52 246 .972 .83 80 4310 8000 52 60 291 299 0 506 221 285 1.084 529 308 .923 1.257 .116 .33
19 3289 2621 175 198 3114 2423 3453 2865 176 205 3278 2667 0 0 1091 775 34 47 100 100 100 100 5537 5945 1.285 .778 .814 .821 .768 1.521 80 342 .755 .95 100 4460 8000 51 61 305 315 0 3013 228 2785 .894 3293 3066 1.118 .935 -.161 -.097
20 801 707 172 201 629 506 805 752 173 205 633 551 0 0 301 254 32 47 96 92 96 88 1135 1184 1.243 .804 .87 .74 .893 2.162 52 234 .818 .86 80 4600 8000 52 60 320 328 0 813 231 582 .925 864 633 1.081 1.001 -.113 .001

Total number of rows: 43008

Table truncated, full table size 9508 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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