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Sample GSM469374 Query DataSets for GSM469374
Status Public on Jan 21, 2010
Title CCL171 + IGF I 24h culture slide 1
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 StratageneRef; RNA for the reference was pooled from 11 cell lines - obtained from Stratagene.; Protocol Type = Biological Sample; Performer: Michal,,Rajski
Label Cy3
Label protocol MessageAmpII; Total RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX), according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
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).; Protocol Type = Labeling; Performer: Michal,,Rajski
 
Channel 2
Source name CCL171 plus IGF I plus doping controls.
Organism Homo sapiens
Characteristics cell line: CCL 171 fibroblasts
Growth protocol Monoculture cell conditions.; MCF - 7 and CCL - 171 cells were expanded and propagated in Dulbeccos Modified Eagles Medium (DMEM) supplemented with: 10% FBS (GIBCO, Grand Island, N.Y.), L - glutamine, 4.5 g/L glucose, 100 U/ml penicillin and 100 ug/ml streptomycin (GIBCO, Grand Island, N.Y.). For mono-culture experiments the cells were cultivated for 6 hours at 30,000 cells/cm2 in DMEM medium with 5% FBS. After 6 hours medium was changed to DMEM medium with 0.2% FBS and the cells were cultured for 48 hours(starving period). After 48 hours medium was changed to a fresh DMEM medium with 0.2% FBS and the cells were cultured for 24 hours.; Protocol Type = Biological Sample; Performer: Michal,,Rajski
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
Label Cy5
Label protocol MessageAmp II; RNA was amplified using the Message AmpTM II aRNA Kit (Ambion, Austin, TX) according to the manufacturer's instructions.; Protocol Type = Amplification; Performer: Michal,,Rajski
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).; Protocol Type = Labeling; Performer: Michal,,Rajski
 
 
Hybridization protocol not provided
Scan protocol GenePix 4100A 01
Description Simple annotation: Stimulation, Control experiment
Image: http://smd.stanford.edu/MicroArray/gifs/2006-12/71308.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 Nov 09, 2009
Last update date Jan 21, 2010
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 GPL9550
Series (2)
GSE18954 Effects of IGF 1 on CCL-171 fibroblasts
GSE18955 Effects of IGF 1 on primary breast fibroblasts, MCF-7 breast cancer cells and CCL-171 fibroblasts

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 16012 65080 889 727 15123 64353 16356 65535 888 747 15467 64808 0 92 1641 2320 154 161 100 100 100 100 79476 80275 .235 4.255 4.19 4.289 4.19 1.117 52 358 4.254 .99 90 1760 6160 39 48 44 53 -100 66518 743 65775 4.349 66983 66240 .23 4.283 2.121 2.099
2 18881 65074 880 738 18001 64336 19338 65535 886 770 18458 64797 0 96 2495 2364 169 216 100 100 100 100 82337 83255 .28 3.574 3.511 3.647 3.511 1.248 52 298 3.564 .99 90 1910 6160 39 48 59 68 -100 66512 754 65758 3.653 66983 66229 .274 3.588 1.869 1.843
3 43888 61363 827 709 43061 60654 46692 65535 837 731 45865 64826 0 75 9537 11674 121 193 100 100 100 100 103715 110691 .71 1.409 1.413 1.442 1.407 1.289 80 332 1.4 .99 100 2060 6170 40 50 74 84 -100 62719 725 61994 1.44 66983 66258 .695 1.445 .526 .531
4 17074 58662 839 687 16235 57975 18524 65535 856 700 17685 64848 0 71 5560 14243 145 134 100 100 98 100 74210 82533 .28 3.571 3.667 4.091 3.549 1.912 80 335 3.517 .98 100 2220 6160 39 49 90 100 -100 59958 702 59256 3.65 66983 66281 .274 3.748 1.868 1.906
5 8163 4844 920 687 7243 4157 8009 4741 968 725 7089 4054 0 0 907 551 404 211 100 100 100 100 11400 11143 1.742 .574 .572 .573 .57 1.129 52 286 .503 .96 90 2360 6160 39 48 104 113 0 4951 702 4249 .587 4846 4144 1.705 .585 -.77 -.775
6 61495 64747 885 705 60610 64042 65535 65535 1034 897 64650 64830 73 96 11704 3985 1173 1578 100 100 98 100 124652 129480 .946 1.057 1.003 1.118 1.003 1.546 52 307 1.034 .98 90 2510 6160 39 48 119 128 -100 66178 721 65457 1.08 66983 66263 .926 1.025 .111 .036
7 2113 1907 838 702 1275 1205 2010 1863 941 862 1172 1161 0 0 564 300 1152 1621 57 5 3 0 2480 2333 1.058 .945 .991 .969 .961 1.315 52 288 .846 .87 90 2660 6170 40 49 134 143 0 1949 718 1232 .966 1904 1187 1.035 1.013 -.05 .018
8 39516 54662 876 702 38640 53960 47330 65535 921 772 46454 64833 0 71 16401 20345 611 966 98 100 93 97 92600 111287 .716 1.396 1.396 1.591 1.372 1.811 80 371 1.37 .99 100 2820 6160 39 49 150 160 -100 55870 718 55152 1.427 66983 66266 .701 1.426 .513 .512
9 14167 62657 889 718 13278 61939 14302 63495 916 745 13413 62777 0 13 1760 4045 197 217 100 100 100 100 75217 76190 .214 4.665 4.68 4.721 4.604 1.138 52 295 4.52 .95 90 2970 6160 39 48 165 174 -100 64042 734 63308 4.768 64898 64164 .21 4.784 2.253 2.258
10 6419 3789 892 716 5527 3073 6818 3894 915 749 5926 3178 0 0 1624 740 167 209 98 100 97 100 8600 9104 1.799 .556 .536 .599 .55 1.693 80 356 .534 .97 100 3120 6170 40 50 180 190 0 3873 732 3141 .568 3980 3248 1.76 .548 -.815 -.867
11 61076 64565 886 729 60190 63836 65535 65535 991 905 64649 64806 69 90 11682 4146 707 1370 100 100 100 100 124026 129455 .943 1.061 1.002 1.104 1.002 1.379 52 301 1.047 .98 90 3270 6160 39 48 195 204 -100 65992 745 65247 1.084 66983 66238 .923 1.025 .116 .035
12 2093 1710 878 705 1215 1005 2127 1760 1273 893 1249 1055 0 0 526 378 1840 1313 2 16 1 0 2220 2304 1.209 .827 .845 .84 .859 1.613 80 358 .635 .61 100 3430 6160 39 49 211 221 0 1748 721 1027 .845 1799 1078 1.183 .863 -.242 -.212
13 1639 1218 892 703 747 515 1644 1207 1400 807 752 504 0 0 146 189 2182 539 0 40 0 0 1262 1256 1.45 .689 .67 .635 .671 1.875 52 248 .229 .75 80 3580 6160 40 48 227 235 0 1245 719 526 .705 1234 515 1.419 .685 -.505 -.546
14 1390 1044 884 680 506 364 1395 1014 897 687 511 334 0 0 141 125 208 127 100 96 71 82 870 845 1.39 .719 .654 .701 .753 1.555 52 246 .633 .65 80 3730 6160 40 48 242 250 0 1067 695 372 .735 1036 341 1.36 .668 -.444 -.582
15 8084 2440 861 677 7223 1763 8220 2476 855 685 7359 1799 0 0 895 283 138 117 100 100 100 100 8986 9158 4.097 .244 .244 .244 .249 1.205 52 277 .234 .97 90 3890 6160 39 48 257 266 0 2494 692 1802 .249 2531 1839 4.008 .25 -2.003 -2.001
16 1472 1074 937 683 535 391 1465 1097 963 690 528 414 0 0 154 172 158 121 100 96 92 78 926 942 1.368 .731 .784 .671 .675 1.861 52 274 .729 .67 90 4030 6160 39 48 271 280 0 1098 698 400 .747 1121 423 1.339 .801 -.421 -.319
17 1327 1021 813 684 514 337 1358 1037 823 687 545 353 0 0 160 157 152 118 98 92 86 75 851 898 1.525 .656 .648 .604 .636 2.404 52 213 .639 .59 80 4180 6170 41 49 287 295 0 1044 699 344 .67 1060 361 1.492 .662 -.577 -.595
18 1116 1031 706 679 410 352 1110 1035 721 689 404 356 0 0 146 147 136 114 97 95 83 82 762 760 1.165 .859 .881 .879 .87 2.062 80 293 .041 .14 100 4340 6170 40 50 302 312 0 1054 694 360 .878 1058 364 1.14 .901 -.189 -.151
19 3293 2315 708 688 2585 1627 3346 2315 750 711 2638 1627 0 0 469 293 340 145 100 100 100 100 4212 4265 1.589 .629 .617 .633 .611 1.236 52 270 .615 .96 90 4480 6160 39 48 316 325 0 2366 703 1663 .643 2366 1663 1.554 .63 -.636 -.666
20 2670 2573 740 715 1930 1858 2573 2582 777 727 1833 1867 0 0 401 302 320 139 100 100 100 100 3788 3700 1.039 .963 1.019 .966 1.014 1.188 52 322 .9 .91 90 4640 6160 39 48 332 341 0 2630 731 1899 .984 2639 1908 1.016 1.041 -.023 .058

Total number of rows: 44544

Table truncated, full table size 10175 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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