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Sample GSM116330 Query DataSets for GSM116330
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, b4 corresponds to replicate 6
Sample type RNA
 
Channel 1
Source name FGF-control-b4
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 Cy3
Label protocol labeled with Genisphere's 3DNA Array 900 Cy3/Cy5 kit
 
Channel 2
Source name FGF-t320-b4
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 Cy5
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 2.356 2779 2339 1286 56 63 32 100 100 0 613 1748 2285 81 181 47 83 83 0 5.119 1.369 1.471 2.801 6.163 0.881 0 12 68 3254 3948 2723 531 2282 1666 28070 20985 70.143 33.023 54 61 50 130 76 26 0.255 3431 4008
AB000490 1.655 65 98 127 55 69 28 41 30 0 106 127 80 103 117 50 28 16 0 3.15 1.796 0.619 0.853 4.184 -35.371 0 80 451 13 65 10 3 42 23 7888 10210 1 0.191 130 60 41 63 96 43 0 14 68
AB001423 2.525 237 408 398 50 66 24 83 66 0 111 211 237 78 107 55 41 33 0 5.756 2.696 5.222 3.119 9.225 5.499 0 12 68 218 489 186 32 357 132 4908 2533 14.192 1.882 97 55 36 112 73 51 0.049 231 509
AB001424 2.588 63 153 379 50 65 24 41 30 0 98 130 112 96 114 50 30 18 0 6.014 3.007 0.496 0.713 4.802 10.46 0 80 370 14 137 12 2 103 34 12305 10472 3.654 0.319 246 54 36 85 89 44 0.047 16 144
AB001425 0 68 81 58 62 76 27 33 17 0 135 151 88 140 153 70 23 8 0 -1.503 1.804 0.478 0.495 3.84 7.752 0 80 402 2 29 6 -4 19 10 6561 12071 0.167 -0.031 71 67 36 58 130 45 0.003 3 31
AB001426 -2.185 83 83 39 54 72 26 50 25 0 228 244 142 98 107 42 75 75 0 0.22 0.196 0.157 0.161 2.198 -105.174 0 12 104 158 174 28 130 28 146 1003 2941 0.414 3.256 47 59 37 58 91 39 0 152 167
AB001428 -4.327 3549 2999 2062 48 82 24 100 100 0 70705 63089 16238 114 1774 64 100 100 75 0.05 0.047 0.05 0.027 3.067 0.043 0 12 104 74090 65926 3500 70590 2951 62975 35986 757070 121.038 947.183 68 52 29 25 106 3 0.734 69206 61554
AB001430 0 50 65 58 50 65 25 30 10 0 129 174 226 97 112 50 41 26 0 0 0.191 0.473 0.459 3.818 0.369 0 80 409 32 91 0 32 14 77 5279 13994 0 1.234 88 55 39 129 90 45 0.013 30 88
AB001431 0 46 168 474 46 69 23 35 26 0 114 181 278 110 148 65 23 12 0 0 1.718 0.407 0.517 4.644 3.591 0 80 399 4 193 0 4 122 71 13491 14496 4.28 0.492 281 50 33 153 102 44 0.083 4 198
AB001432 -3.881 50 68 68 48 73 25 33 13 0 138 190 293 97 116 51 47 27 0 0.068 0.217 0.438 0.351 3.735 -0.012 0 80 416 42 113 2 40 20 93 5488 15256 -0.185 1.438 100 52 34 153 90 44 0 41 109
AB001434 0 45 84 149 51 208 26 30 21 0 113 167 260 89 308 48 40 28 0 -0.273 0.418 0.68 0.507 3.996 0.04 0 80 422 17 109 -6 23 32 77 6717 13368 -4.621 -2.911 176 56 12 155 83 15 0.027 15 107
AB001435 -6.863 581 1061 1226 57 74 30 100 91 0 60645 58172 11258 111 206 57 100 100 16 0.009 0.017 0.013 0.009 3.083 0.016 0 12 104 61057 59064 523 60534 1003 58061 12729 698080 32.273 1013.736 115 62 41 19 103 27 0.395 56673 54899
AB001436 0.781 75 230 386 49 81 25 41 41 0 143 175 145 128 207 76 33 16 0 1.718 3.827 0.533 0.552 2.482 0.251 0 12 94 40 228 25 15 181 47 2768 2103 5.75 -0.408 167 53 31 82 119 36 0.192 42 240
AB001456 0.519 1543 1530 890 60 95 41 91 91 0 1131 1611 1703 97 131 56 83 83 0 1.433 0.971 1.899 1.715 5.139 0.266 0 12 104 2516 2984 1482 1034 1470 1514 18360 19340 34.4 26.385 58 65 43 105 90 42 0.119 2559 2990
AB001457 0.08 1838 2029 1161 49 73 23 100 100 0 1792 2923 3321 98 102 48 91 91 0 1.057 0.701 0.564 0.891 2.694 0.567 0 12 104 3482 4805 1789 1693 1980 2825 24362 35088 84.44 58.111 57 53 31 113 91 47 0.631 3501 4756
AB001737 -2.124 60 87 85 49 98 23 42 27 0 138 179 198 89 115 45 51 31 0 0.229 0.424 0.673 0.608 3.277 -109.133 0 80 432 59 127 11 48 38 89 7003 14326 -0.48 1.405 97 53 23 110 83 39 0 57 124
AB001738 -0.759 72 95 96 62 87 33 32 22 0 158 188 126 141 173 77 32 15 0 0.591 0.703 0.573 0.614 3.516 0.01 0 80 360 27 80 10 17 33 47 7610 15104 0.25 0.194 100 67 38 66 131 44 0 27 80
AB002663 1.321 616 816 597 58 74 26 91 91 0 327 1117 1456 104 116 57 66 66 0 2.498 0.748 1.479 1.664 12.391 0.605 0 12 104 780 1771 557 223 758 1013 9803 13411 27.621 17.509 73 63 36 130 97 49 0.006 809 1757
AB003502 0 137 674 1201 74 90 40 58 45 0 149 405 816 157 193 75 33 23 0 -8.345 2.42 0.922 1.042 4.534 2.015 0 80 399 56 848 63 -7 600 248 54015 32431 14.318 2.814 178 80 44 201 146 39 0.359 61 878
AB005457 1.163 14630 15273 5160 76 109 42 100 100 0 6648 8304 5749 148 182 73 100 100 0 2.24 1.863 2.349 2.25 1.608 1.204 0 12 104 21052 23352 14553 6499 15197 8155 183285 99653 355.674 110.706 33 83 38 69 138 40 0.669 21726 23955

Total number of rows: 21582

Table truncated, full table size 4171 Kbytes.




Supplementary data files not provided
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