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Sample GSM81150 Query DataSets for GSM81150
Status Public on May 14, 2009
Title HS 129 human poorly diff. liposarcoma, LiSa-2 cells, 0 hrs no treatment
Sample type mixed
 
Channel 1
Source name human reference RNA
Organism Homo sapiens
Characteristics As a control RNA we used a set of human clones. The clones were grown individually. The cell clusters were pooled together and a sample of this total pool was used to extract the plasmid DNA (Qiagen HiSpeed plasmid midi kit, Cat. no. 12643, following the manufacturer's recommendations).
Growth protocol All clones of the human set were grown individually in 100 micro liters of appropriate cell culture media, OVN at 37 degrees C., in a 384-well plate. The cell cultures were pooled together and a sample of this total pool was used to extract the plasmid DNA (Qiagen HiSpeed plasmid midi kit, Cat. no. 12643, following the manufacturer's recommendations).
Extracted molecule other
Extraction protocol The plasmid DNA originated from all clones of the set. It was linearized by a two-step PCR protocol and used to produce an 'in vitro' RNA. This RNA was labeled and hybridized. For details see http://madb.eng.uiowa.edu/MICROARRAY/HTML/protocols
Label cy5
Label protocol RNA labeling was performed using the Genisphere 3DNA-350 indirect labeling kit. Reference RNA (440 ng) was reverse transcribed using reverse transcript RT dT primers. The synthesized tagged cDNA was hybridized with PCR products printed on the slides. The fluorescent cDNA reagent (capture sequence for Cy3 or Cty5) were hybridized to the cDNA based on the complementarity to a sequence of the 5' end of the RT primer.
 
Channel 2
Source name Poorly diff. liposarcoma, LiSa-2 cells
Organism Homo sapiens
Characteristics Poorly diff. liposarcoma, LiSa-2 cells
Growth protocol Cells were grown in penicillin streptomycin containing media IMDM + 10% FBS (100 U/ml) for 48 hrs at 37 degrees C. This represents time zero hr.
Extracted molecule total RNA
Extraction protocol RNA was extracted using the Qiagen RNeasy kit protocol for isolation of total RNA from tissues with addition of DNase treatment and an additional digestion with proteinase K, Trizol extraction, ethanol precipitation. For details see http://madb.eng.uiowa.edu/MICROARRAY/HTML/protocols/UI_human_37K/RNA_purification_protocol.htm
Label cy3
Label protocol RNA labeling was performed using the Genisphere 3DNA-350 indirect labeling kit. The total RNA (2 micrograms) was reversed transcribed using reverse transcript RT dT primers. The synthesized tagged cDNA was hybridized with PCR products printed on the slides. The fluorescent cDNA reagents (capture sequence for Cy3 or Cy54) were hybridized to the cDNA based on the complementarity to a sequence of the 5' end of the RT primer.
 
 
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B fluorescent scanner and image intensity data were extracted and analyzed with GenePix Pro 3.0 analysis software.
Description Poorly diff. liposarcoma, LiSa-2 cells.
Data processing raw data as output from GenePix Pro 3.0 analysis software
 
Submission date Oct 31, 2005
Last update date May 14, 2008
Contact name Bartley Joseph Brown
E-mail(s) bbrown@eng.uiowa.edu
Phone 319 335 6432
Organization name The University of Iowa
Lab CBCB
Street address 5317
City Iowa City
State/province IA
ZIP/Postal code 52242
Country USA
 
Platform ID GPL2822
Series (1)
GSE3643 Poorly differentiated, human liposarcoma LiSa-2 cell line response to the synthetic triterpenoid CDDO

Data table header descriptions
ID_REF
VALUE log2 of PRE_VALUE
X The X-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Y The Y-coordinate in µm of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image.
Dia. The diameter in µm of the feature-indicator.
F635 Median Median feature pixel intensity at wavelength #1 (635 nm).
F635 Mean Mean feature pixel intensity at wavelength #1 (635 nm).
F635 SD The standard deviation of the feature pixel intensity at wavelength #1 (635 nm).
F635 CV The coefficient of variation of feature pixel intensity.
B635 The actual background value used for the feature in GenePix Pro calculations (as opposed to B635 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B635 is different to B635 Median.
B635 Median The median feature background intensity at wavelength #1 (635 nm).
B635 Mean The mean feature background intensity at wavelength #1 (635 nm).
B635 SD The standard deviation of the feature background intensity at wavelength #1 (635 nm).
B635 CV The coefficient of variation of local background pixel intensity.
% > B635+1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm).
% > B635+2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm).
F635 % Sat. The percentage of feature pixels at wavelength #1 that are saturated.
F532 Median Median feature pixel intensity at wavelength #2 (532 nm).
F532 Mean Mean feature pixel intensity at wavelength #2 (532 nm).
F532 SD The standard deviation of the feature intensity at wavelength #2 (532 nm).
F532 CV The coefficient of variation of local background pixel intensity.
B532 The actual background value used for the feature in GenePix Pro calculations (as opposed to B532 Median, for example, which is the local median background.) This column is required because GenePix Pro 5.0 has global and negative control background subtraction methods. If you choose a non-local method, B532 is different to B532 Median.
B532 Median The median feature background intensity at wavelength #2 (532 nm).
B532 Mean The mean feature background intensity at wavelength #2 (532 nm).
B532 SD The standard deviation of the feature background intensity at wavelength #2 (532 nm).
B532 CV The coefficient of variation of feature pixel intensity.
% > B532+1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm).
% > B532+2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm).
F532 % Sat. The percentage of feature pixels at wavelength #2 that are saturated.
Ratio of Medians (635/532) The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.
Median of Ratios (635/532) The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Mean of Ratios (635/532) The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.
Ratios SD (635/532) The geometric standard deviation of the pixel intensity ratios.
Rgn Ratio (635/532) The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.
Rgn R2 (635/532) The coefficient of determination for the current regression value.
F Pixels The total number of feature pixels.
B Pixels The total number of background pixels.
Circularity A measure of circularity from 0 to 100, using a metric based on the variance of the distance of each boundary pixel to the centroid of the feature: 100 is most circular, 0 is most non-circular. Circular features always have a circularity of 100, square features always have a circularity of 79 (= p/4*100).
Sum of Medians (635/532) The sum of the median intensities for each wavelength, with the median background subtracted.
Sum of Means (635/532) The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.
Log Ratio (635/532) Log (base 2) transform of the ratio of the medians.
F635 Median - B635 The median feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Median - B532 The median feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Mean - B635 The mean feature pixel intensity at wavelength #1 with the median background subtracted.
F532 Mean - B532 The mean feature pixel intensity at wavelength #2 with the median background subtracted.
F635 Total Intensity The sum of feature pixel intensities at wavelength #1.
F532 Total Intensity The sum of feature pixel intensities at wavelength #2.
SNR 635 The signal-to-noise ratio of the feature, calculated as (F635 Mean - B635 Mean) / B635 SD.
SNR 532 The signal-to-noise ratio of the feature, calculated as (F532 Mean - B532 Mean) / B532 SD.
Flags The type of flag associated with a feature.
Normalize The normalization status of the feature (included/not included).
Autoflag Reports whether or not a feature has been flagged from the Flag Features dialog box. It applies to good and bad flags only.
UNF_VALUE Ratio of means, the ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.
PRE_VALUE same as UNF_VALUE but with flagged values removed

Data table
ID_REF VALUE X Y Dia. F635 Median F635 Mean F635 SD F635 CV B635 B635 Median B635 Mean B635 SD B635 CV % > B635+1SD % > B635+2SD F635 % Sat. F532 Median F532 Mean F532 SD F532 CV B532 B532 Median B532 Mean B532 SD B532 CV % > B532+1SD % > B532+2SD F532 % Sat. Ratio of Medians (635/532) Median of Ratios (635/532) Mean of Ratios (635/532) Ratios SD (635/532) Rgn Ratio (635/532) Rgn R2 (635/532) F Pixels B Pixels Circularity Sum of Medians (635/532) Sum of Means (635/532) Log Ratio (635/532) F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 Flags Normalize Autoflag UNF_VALUE PRE_VALUE
1_1_1 -0.5208 2320 11525 115 5836 5943 1877 31 44 44 61 69 113 100 100 0 8318 8521 2501 29 59 59 75 91 121 100 100 0 0.701 0.692 0.687 1.450 0.689 0.885 461 2470 93 14051 14361 -0.512 5792 8259 5899 8462 2739772 3928025 85.246 92.813 0 0 0 0.697 0.697
1_2_1 -0.0145 2485 11525 105 25024 24066 6810 28 44 44 59 60 101 100 100 0 24948 24335 6100 25 62 62 77 104 135 100 100 0 1.004 0.999 0.968 1.289 1.002 0.961 370 1847 96 49866 48295 0.005 24980 24886 24022 24273 8904490 9003790 400.117 233.250 0 0 0 0.990 0.990
1_3_1 -0.0559 2655 11520 120 5829 11582 10746 92 47 47 65 73 112 100 100 0 6072 12053 10931 90 62 62 85 122 143 100 100 0 0.962 0.950 0.931 1.458 0.973 0.968 467 2268 94 11792 23526 -0.056 5782 6010 11535 11991 5408575 5628772 157.767 98.098 0 0 0 0.962 0.962
1_4_1 -0.0664 2800 11520 110 20996 27564 16919 61 50 50 77 101 131 100 100 0 20008 28871 17668 61 63 63 87 111 127 100 100 0 1.050 0.968 0.955 1.303 0.956 0.978 459 1773 94 40891 56322 0.071 20946 19945 27514 28808 12651647 13251991 272.149 259.315 0 0 0 0.955 0.955
1_5_1 -0.3292 2955 11520 115 4261 4477 1639 36 46 46 66 85 128 100 100 0 5438 5627 1889 33 62 62 78 81 103 100 100 0 0.784 0.800 0.788 1.535 0.788 0.823 452 2051 89 9591 9996 -0.351 4215 5376 4431 5565 2023391 2543200 51.894 68.506 0 0 0 0.796 0.796
1_6_1 -0.0189 3120 11515 105 6483 5951 3014 50 45 45 58 51 87 100 100 0 6483 6041 2580 42 59 59 74 77 104 100 100 0 1.002 0.980 0.921 1.533 1.032 0.873 411 1751 93 12862 11888 0.003 6438 6424 5906 5982 2445908 2482707 115.549 77.494 0 0 0 0.987 0.987
1_7_1 -0.3511 3275 11520 115 11284 13755 7536 54 47 47 63 71 112 100 100 0 14648 17539 9797 55 62 62 78 90 115 100 100 0 0.770 0.796 0.792 1.318 0.776 0.962 445 2013 90 25823 31185 -0.376 11237 14586 13708 17477 6121009 7804667 192.845 194.011 0 0 0 0.784 0.784
1_8_1 -0.1681 3435 11520 115 8407 8893 4651 52 48 48 65 67 103 100 100 0 8860 9998 5203 52 62 62 81 101 124 100 100 0 0.950 0.889 0.891 1.394 0.888 0.941 440 1943 92 17157 18781 -0.074 8359 8798 8845 9936 3912932 4399151 131.761 98.188 0 0 0 0.890 0.890
1_9_1 -0.4093 3595 11520 120 2371 2431 964 39 46 46 64 78 121 100 100 0 3123 3229 1145 35 60 60 77 88 114 100 100 0 0.759 0.737 0.741 1.661 0.737 0.759 450 2157 96 5388 5554 -0.398 2325 3063 2385 3169 1093804 1453216 30.346 35.818 0 0 0 0.753 0.753
1_10_1 -0.0679 3755 11515 110 7060 7010 2097 29 44 44 62 70 112 100 100 0 7342 7358 2072 28 59 59 77 99 128 100 100 0 0.963 0.969 0.947 1.398 0.958 0.910 439 1925 90 14299 14265 -0.054 7016 7283 6966 7299 3077526 3230029 99.257 73.545 0 0 0 0.954 0.954
1_11_1 -0.2567 3915 11525 110 1411 1794 1415 78 43 43 59 65 110 98 97 0 1526 2152 1717 79 59 59 73 83 113 99 98 0 0.933 0.866 0.832 2.337 0.809 0.780 437 1737 91 2835 3844 -0.101 1368 1467 1751 2093 783910 940284 26.692 25.048 0 0 0 0.837 0.837
1_12_1 -0.0277 4060 11515 105 12690 15604 8810 56 45 45 62 77 124 100 100 0 13573 15922 8427 52 60 60 76 91 119 100 100 0 0.936 0.985 0.959 1.332 1.001 0.959 429 1769 91 26158 31421 -0.096 12645 13513 15559 15862 6694185 6830437 201.844 174.132 0 0 0 0.981 0.981
1_13_1 -0.3183 4220 11525 80 119 181 191 105 43 43 60 88 146 40 20 0 170 229 227 99 57 57 70 91 130 60 26 0 0.673 0.328 0.453 5.922 1.729 0.171 15 1501 2 189 310 -0.572 76 113 138 172 2719 3430 1.375 1.747 0 0 0 0.802 0.802
1_14_1 4390 11525 100 42 51 41 80 42 42 55 56 101 4 1 0 58 67 78 116 56 56 67 81 120 1 1 0 0.000 1.000 1.049 4.614 2.201 0.062 316 1902 100 2 20 Error 0 2 9 11 16113 21283 -0.071 0.000 -50 0 0 0.818
1_15_1 4545 11525 100 44 54 47 87 43 43 57 59 103 5 1 0 57 62 30 48 56 56 74 121 163 1 0 0 1.000 1.095 1.156 4.977 0.150 0.050 316 1911 100 2 17 0.000 1 1 11 6 17100 19634 -0.051 -0.099 -50 0 0 1.833
1_16_1 -0.3529 4675 11515 50 52 163 311 190 44 44 58 67 115 12 12 0 195 209 88 42 57 57 73 100 136 87 25 0 0.058 0.118 0.060 4.770 0.328 0.043 8 614 44 146 271 -4.109 8 138 119 152 1300 1672 1.567 1.360 0 0 0 0.783 0.783
1_17_1 4865 11525 100 43 57 47 82 43 43 64 116 181 1 0 0 57 62 26 41 57 57 86 184 213 0 0 0 0.000 1.225 1.181 3.927 0.874 0.207 316 1951 100 0 19 Error 0 0 14 5 18092 19558 -0.060 -0.130 -50 0 0 2.800
1_18_1 5025 11525 100 42 53 52 98 42 42 58 93 160 1 0 0 55 68 91 133 57 57 74 147 198 1 0 0 0.000 1.000 0.930 3.462 0.364 0.185 316 1796 100 -2 22 Error 0 -2 11 11 16832 21407 -0.054 -0.041 -50 0 0 1.000
1_19_1 5185 11525 100 43 53 32 60 42 42 54 47 87 8 2 0 57 63 46 73 56 56 67 72 107 1 1 0 1.000 1.000 1.157 4.217 0.237 0.106 316 1855 100 2 18 0.000 1 1 11 7 16599 20057 -0.021 -0.056 -50 0 0 1.571
1_20_1 0.2774 5330 11520 70 128 180 180 100 43 43 61 86 140 45 28 0 77 169 218 128 56 56 70 89 127 25 14 0 4.048 1.955 2.110 8.014 1.041 0.027 35 1116 40 106 250 2.017 85 21 137 113 6294 5920 1.384 1.112 0 0 0 1.212 1.212

Total number of rows: 37632

Table truncated, full table size 8659 Kbytes.




Supplementary data files not provided
Processed data not provided for this record
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