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Sample GSM116320 Query DataSets for GSM116320
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, A5 corresponds to replicate 2
Sample type RNA
 
Channel 1
Source name FGF-control-a5
Organism Mus musculus
Characteristics Differentiated gestational Day 12.5 Mouse cortical-derived neurospheres (control)
Treatment protocol Neurospheres differentiated by the removal of EGF and LIF from the mitogenic media (control)
Growth protocol Neurospheres were cultured in serum-free mitogenic medium DMEM/F-12, 20ng/ml basic Fibroblast Growth Factor, 20ng/ml human recombinant Epidermal Growth Factor, 0.15ng/ml human recombinant Leukemia Inhibitory Factor, 1X Insulin-Transferrin-Selenium-X Supplement, 5ug/ml heparin, and 20nM progesterone and cultured at 37C (5% CO2) in a humidified chamber to allow formation of neurospheres
Extracted molecule total RNA
Extraction protocol Invitrogen's Trizol method followed by purification with Qiagen's RNeasy kit
Label Cy5
Label protocol labeled with Genisphere's 3DNA Array 900 Cy3/Cy5 kit
 
Channel 2
Source name FGF-t320-a5
Organism Mus musculus
Characteristics Differentiated gestational Day 12.5 Mouse cortical-derived neurospheres pre-exposed to 320mg/dl ethanol (treatment)
Treatment protocol Following treatment with 320mg/dl ethanol in mitogenic media, neurospheres were differentiated by the removal of EGF and LIF from the mitogenic media for 3 days without ethanol (treatment)
Growth protocol Neurospheres were grown in mitogenic media and supplemented with 320mg/dl ethanol for 5 days prior to differentiation
Extracted molecule total RNA
Extraction protocol Invitrogen's Trizol method followed by purification with Qiagen's RNeasy kit
Label Cy3
Label protocol A total of 1ug of total RNA was reverse-transcribed with Superscript II (Invitrogen) using primers for Cy3 and Cy5 according to the 3DNA Array 900 Cy3/Cy5 protocol (Genisphere).
 
 
Hybridization protocol Hybridization was performed as stated in Genisphere's 3DNA Array 900 manual
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 6.0.1.25 analysis software
Description Differentiated gestational Day 12.5 Mouse cortical-derived neurospheres
Data processing After background correction and removal of flagged values, background corrected intensities were normalized to the mean-of-ratios
 
Submission date Jun 26, 2006
Last update date Dec 03, 2021
Contact name Rajesh Miranda
E-mail(s) rmiranda@tamu.edu
Organization name Texas A&M University
Street address 8447 Riverside Parkway
City Bryan
ZIP/Postal code 77807
Country USA
 
Platform ID GPL3919
Series (1)
GSE5152 Gene expression changes in differentiated cortical neurospheres pre-exposed to ethanol

Data table header descriptions
ID_REF GEO Accession number
VALUE Normalized log2 ratio of means defined as CH2 divided by CH1
F635 Median
F635 Mean
F635 SD
B635 Median
B635 Mean
B635 SD2
% > B635+1SD2
% > B635+2SD2
F635 % Sat.
F532 Median
F532 Mean
F532 SD
B532 Median
B532 Mean
B532 SD2
% > B532+1SD2
% > B532+2SD2
F532 % Sat.
Ratio of Medians (532/635)
Ratio of Means (532/635)
Median of Ratios (532/635)
Mean of Ratios (532/635)
Ratios SD (532/635)
Rgn Ratio (532/635)
Rgn R2 (532/635)
F Pixels
B Pixels
Sum of Medians
Sum of Means
F635 Median - B635
F532 Median - B532
F635 Mean - B635
F532 Mean - B532
F635 Total Intensity
F532 Total Intensity
SNR 635
SNR 532
F635 CV
B635
B635 CV
F532 CV
B532
B532 CV
Rgn R2 (532/635)
Sum of Medians (532/635)
Sum of Means (532/635)

Data table
ID_REF VALUE F635 Median F635 Mean F635 SD B635 Median B635 Mean B635 SD2 % > B635+1SD2 % > B635+2SD2 F635 % Sat. F532 Median F532 Mean F532 SD B532 Median B532 Mean B532 SD2 % > B532+1SD2 % > B532+2SD2 F532 % Sat. Ratio of Medians (532/635) Ratio of Means (532/635) Median of Ratios (532/635) Mean of Ratios (532/635) Ratios SD (532/635) Rgn Ratio (532/635) Rgn R2 (532/635) F Pixels B Pixels Sum of Medians Sum of Means F635 Median - B635 F532 Median - B532 F635 Mean - B635 F532 Mean - B532 F635 Total Intensity F532 Total Intensity SNR 635 SNR 532 F635 CV B635 B635 CV F532 CV B532 B532 CV Rgn R2 (532/635) Sum of Medians (532/635) Sum of Means (532/635)
AB000121 -0.226 8504 7001 3555 37 53 18 100 100 0 7362 6067 4113 127 151 69 100 100 0 0.855 0.853 0.8 0.65 4.532 0.95 0 12 104 15702 12903 8467 7235 6963 5940 84010 72816 376.04 85.725 50 51 34 67 94 45 0.62 16805 13813
AB000490 -0.493 342 400 427 42 56 17 83 83 0 362 699 810 148 169 75 66 58 0 0.71 1.536 3.6 2.146 15.191 2.846 0 12 104 513 908 300 213 358 550 4808 8391 19.417 7 106 57 31 115 110 44 0.097 565 892
AB001423 -2.26 71 260 554 45 62 22 51 38 0 139 262 560 133 225 67 28 15 0 0.209 0.597 1.828 1.313 14.607 0.685 0 80 420 30 343 25 5 215 128 20875 20984 8.677 0.54 212 62 36 213 99 29 0.292 39 386
AB001424 -0.382 70 152 282 47 62 22 50 36 0 146 284 568 128 144 66 37 20 0 0.767 1.472 2.241 2.144 8.711 3.743 0 80 385 39 260 22 17 105 155 12225 22713 3.935 2.102 184 64 36 200 95 45 0.011 44 258
AB001425 0 67 106 231 51 66 27 41 20 0 184 204 124 186 205 98 27 10 0 -0.174 0.322 2.774 2.152 6.746 0.181 0 80 379 13 71 15 -2 54 17 8527 16372 1.459 -0.014 217 70 41 60 138 48 0.023 19 87
AB001426 1.476 140 305 325 40 61 17 75 58 0 415 890 1167 138 150 82 83 66 0 2.782 2.836 2.529 2.012 13.666 4.919 0 12 104 376 1017 99 277 265 752 3667 10676 13.792 8.967 106 55 28 131 102 54 0.304 340 915
AB001428 3.653 6588 5280 4676 53 73 28 84 81 0 82340 58902 36983 140 338 78 93 90 50 12.578 11.243 10.59 16.233 14.027 10.634 0 32 170 88733 63987 6534 82199 5226 58761 168950 1884886 185.395 746.172 88 73 38 62 104 23 0.824 69587 50496
AB001430 2.413 60 119 186 52 71 29 33 23 0 170 288 438 127 148 63 46 27 0 5.327 2.395 2.644 2.009 7.12 0.877 0 80 399 51 228 8 43 67 161 9557 23111 1.625 2.191 155 71 41 152 94 42 0.049 43 210
AB001431 0.536 65 320 792 47 75 25 46 33 0 212 309 457 186 224 102 27 15 0 1.45 0.45 1.903 1.465 13.906 0.284 0 80 410 42 396 17 25 273 123 25685 24792 9.486 0.829 247 64 34 147 138 45 0.143 43 461
AB001432 0.873 64 160 337 45 56 22 46 31 0 175 284 450 140 163 75 37 23 0 1.831 1.243 2.324 2.148 17.187 0.346 0 80 352 54 258 19 35 115 143 12839 22737 4.667 1.589 210 61 38 158 104 46 0.027 52 262
AB001434 2.157 63 188 430 46 150 22 48 36 0 223 280 328 147 228 85 44 19 0 4.459 0.934 2.034 1.974 12.868 0.721 0 52 266 91 273 16 75 141 132 9800 14599 1.677 0.603 228 63 15 117 109 37 0.78 79 290
AB001435 4.796 2805 3051 1335 46 67 32 100 100 0 76812 73337 16547 154 162 83 100 100 8 27.788 24.356 27.949 26.158 3.633 34.225 0 12 104 79415 76186 2758 76657 3004 73182 36613 880037 91.773 872.177 43 63 48 22 114 51 0.632 60382 58147
AB001436 0.588 319 536 582 42 69 21 100 83 0 584 1456 1610 167 225 81 83 83 0 1.503 2.606 1.741 1.61 19.832 3.166 0 12 68 693 1782 277 416 494 1288 6434 17473 21.793 15.15 108 57 30 110 124 35 0.11 683 1621
AB001456 -1.516 2678 3309 2603 41 56 21 96 96 0 1054 2706 3204 129 161 78 84 75 0 0.35 0.789 0.394 0.52 7.143 0.683 0 32 207 3560 5843 2636 924 3267 2576 105903 86620 151.759 32.431 78 56 37 118 96 48 0.285 4251 6326
AB001457 -2.407 2630 2802 2457 41 58 20 100 96 0 613 1943 2713 125 150 71 75 62 0 0.189 0.657 0.364 0.319 8.975 0.58 0 32 170 3076 4578 2589 487 2761 1817 89697 62174 132.643 25 87 56 35 139 93 47 0.274 3864 5080
AB001737 2.589 50 90 118 45 61 19 41 31 0 171 200 121 140 156 73 32 18 0 6.017 1.32 1.56 1.654 10.451 0.608 0 80 419 36 104 5 31 45 59 7199 16042 1.444 0.593 131 61 32 60 104 46 0.022 30 105
AB001738 -0.629 80 141 229 55 76 31 43 33 0 211 247 173 194 280 104 31 18 0 0.646 0.61 1.665 1.573 7.986 388.978 0 80 310 41 138 25 16 86 52 11324 19764 2.119 -0.312 161 75 40 69 144 37 0 46 156
AB002663 -0.177 876 1226 984 48 67 23 93 93 0 878 1853 2203 146 179 75 93 84 0 0.884 1.45 0.98 1.315 8.676 1.93 0 32 171 1559 2884 827 732 1177 1707 39262 59324 49.031 22.089 80 66 35 118 108 42 0.468 1661 2856
AB003502 -0.601 15382 12969 9405 71 94 36 100 100 0 10311 12486 12739 220 408 105 100 100 0 0.659 0.95 0.793 0.793 5.494 1.016 0 12 104 25401 25162 15311 10090 12897 12265 155633 149831 348.44 114.423 72 97 39 102 163 25 0.747 28176 26517
AB005457 -1.032 6756 19073 20379 72 118 40 100 100 12 3483 14818 17181 215 293 97 81 81 0 0.489 0.769 0.701 0.504 4.734 0.943 0 32 204 9951 33604 6684 3267 19001 14603 610359 474228 466.364 149.083 106 98 34 115 159 33 0.855 11460 36505

Total number of rows: 21582

Table truncated, full table size 4362 Kbytes.




Supplementary data files not provided
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