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Sample GSM116322 Query DataSets for GSM116322
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, A2r corresponds to replicate 4
Sample type RNA
 
Channel 1
Source name FGF-control-a2r
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 37?C (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-a2r
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 -1.151 3259 3433 1713 37 58 13 100 100 0 1538 2687 2536 87 87 37 100 100 0 0.45 0.766 0.387 0.545 3.328 1.23 0 12 68 4671 5995 3221 1450 3396 2599 41204 32259 247.188 69.344 49 44 23 94 75 42 0.443 5013 6198
AB000490 -2.339 384 510 462 41 45 14 91 75 0 145 316 426 77 84 37 66 50 0 0.198 0.511 0.232 0.491 36.147 -0.077 0 12 68 410 707 343 67 468 239 6124 3798 32.059 6.188 90 49 32 134 66 44 0.005 460 753
AB001423 0.627 46 87 140 39 51 14 40 28 0 85 135 277 74 272 31 32 13 0 1.544 1.275 1.382 1.285 7.979 18.424 0 80 410 16 107 6 10 47 60 6979 10868 2.471 -4.333 161 46 28 204 64 11 0.003 17 108
AB001424 -2.453 359 430 243 37 43 12 100 100 0 146 893 2221 87 108 41 58 41 0 0.183 2.054 0.178 0.24 14.023 46.109 0 12 104 379 1198 321 58 392 806 5165 10721 30.2 19.143 56 44 29 248 75 37 0.005 427 1148
AB001425 1.872 74 763 1979 56 122 25 46 38 0 212 5751 13850 146 841 62 50 35 0 3.661 7.922 3.992 4.188 4.149 9.817 0 80 314 82 6312 17 65 707 5605 61076 460114 25.033 79.075 259 66 20 240 125 7 0.598 77 5613
AB001426 -1.379 192 260 187 43 46 15 100 91 0 147 154 74 90 104 36 58 41 0 0.384 0.298 0.428 0.468 4.306 194.544 0 12 104 206 280 149 57 216 64 3125 1860 13.944 1.387 72 51 33 48 77 34 0.001 224 309
AB001428 5.035 2072 2008 1095 45 75 18 100 100 0 66552 57080 21559 83 847 31 100 100 8 32.791 29.036 33.19 30.912 2.759 29.859 0 12 104 68496 58960 2027 66469 1963 56997 24099 684967 102.909 1777.593 54 53 24 37 71 3 0.804 59106 50947
AB001430 -0.943 259 359 345 36 44 11 91 91 0 186 344 365 70 79 30 83 66 0 0.52 0.85 0.984 0.437 8.875 1.219 0 12 104 337 596 222 115 322 274 4309 4126 26.357 8.692 96 43 26 106 60 38 0.114 360 612
AB001431 -0.138 165 250 290 39 42 15 75 75 0 206 370 325 91 96 35 75 58 0 0.909 1.323 1.29 1.48 5.715 -744.288 0 12 68 240 488 126 114 210 278 2998 4447 13.5 7.8 116 46 36 87 78 36 0 246 485
AB001432 -2.349 386 421 379 40 46 16 91 91 0 148 224 206 80 90 37 100 50 0 0.196 0.378 0.141 0.427 7.804 0.299 0 12 104 413 525 346 67 381 144 5062 2700 23.158 3.594 90 47 35 91 69 41 0.023 464 570
AB001434 2.457 47 75 96 44 143 18 30 20 0 100 147 303 82 272 33 40 20 0 5.491 2.136 2.556 2.481 6.865 3.918 0 80 422 21 95 3 18 30 65 6010 11772 -3.636 -3.69 128 52 13 205 70 12 0.573 20 92
AB001435 5.885 1069 1028 589 39 50 17 96 90 0 60950 51946 25420 76 90 30 100 100 12 59.092 52.437 58.718 49.42 16.549 63.732 0 32 171 61904 52859 1030 60874 989 51870 32899 1662283 57.3 1702.269 57 46 33 48 65 33 0.612 53163 45430
AB001436 0 43 56 50 39 47 15 36 22 0 96 120 133 99 104 38 23 13 0 -0.824 1.235 2.26 2.021 7.031 25.432 0 80 410 1 38 4 -3 17 21 4515 9649 0.556 0.424 89 46 32 110 85 37 0.003 2 38
AB001456 -1.931 616 915 739 38 46 14 93 93 0 228 888 1459 77 110 35 65 56 0 0.262 0.924 0.375 0.419 8.76 1.679 0 32 170 728 1687 577 151 877 810 29294 28433 59.882 22.133 80 45 30 164 66 31 0.336 806 1720
AB001457 0.61 841 1021 629 41 59 18 100 100 0 1295 1476 1295 74 80 30 100 100 0 1.527 1.43 1.344 0.912 6.015 1.109 0 12 68 2019 2380 799 1220 979 1401 12260 17711 51.227 45.808 61 49 31 87 64 37 0.167 1979 2344
AB001737 2.473 60 92 79 41 49 17 50 41 0 183 404 799 79 108 33 75 66 0 5.553 6.445 4.728 4.076 15.267 -115.777 0 12 104 122 374 18 104 50 324 1104 4854 2.5 8.69 86 49 34 197 68 31 0.001 111 336
AB001738 1.194 44 62 58 41 54 17 31 20 0 97 171 534 91 106 36 31 12 0 2.288 3.889 2.615 2.354 8.857 869.975 0 80 329 7 99 2 5 20 79 4957 13641 0.429 1.774 93 49 32 312 78 34 0 8 92
AB002663 -0.679 270 344 270 41 46 17 91 91 0 239 417 444 96 100 41 83 75 0 0.625 1.06 1.093 0.737 10.031 0.822 0 12 104 370 623 228 142 302 321 4134 5005 17.45 7.714 78 49 36 106 82 40 0.083 390 629
AB003502 -0.47 1986 2093 1305 46 56 20 100 100 0 1517 2262 1807 115 152 50 100 100 0 0.722 1.049 0.883 0.994 3.328 1.15 0 12 68 3340 4192 1939 1401 2046 2146 25127 27146 99.458 41.884 62 55 36 79 99 33 0.49 3469 4230
AB005457 -0.251 6041 5337 3090 51 65 22 100 100 0 5157 4635 3144 123 132 49 83 83 0 0.84 0.854 0.756 0.454 6.382 0.884 0 12 104 11024 9798 5990 5034 5286 4512 64057 55619 237.577 91.5 57 60 33 67 105 37 0.799 11316 10045

Total number of rows: 21582

Table truncated, full table size 4164 Kbytes.




Supplementary data files not provided
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