NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM116332 Query DataSets for GSM116332
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, b1r corresponds to replicate 8
Sample type RNA
 
Channel 1
Source name FGF-control-b1r
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-b1r
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 0.356 3102 3273 2190 40 58 15 100 100 0 2455 2467 1707 62 69 31 100 91 0 1.28 1.345 1.655 2.063 3.066 1.507 0 12 68 5455 5637 3062 2393 3233 2404 39281 29602 202.588 77.172 66 43 26 69 58 44 0.562 5515 5709
AB000490 -0.893 54 71 46 34 41 8 75 58 0 95 112 84 58 64 24 58 41 0 0.539 0.697 0.36 0.484 3.151 42.164 0 12 68 55 90 19 36 37 53 864 1351 3.667 1.957 64 37 20 75 55 38 0.002 55 90
AB001423 1.232 183 282 253 42 61 17 91 58 0 125 164 147 65 91 32 75 50 0 2.349 2.408 0.847 1.492 6.311 129.837 0 12 104 199 338 140 59 239 99 3393 1975 12.474 2.3 89 46 28 89 61 35 0 207 350
AB001424 3.005 280 395 449 39 52 14 75 75 0 85 87 35 55 64 21 66 25 0 8.029 11.095 7.32 3.682 7.171 -40.971 0 12 104 269 388 240 29 356 32 4744 1049 24.533 1.1 113 42 26 40 52 33 0.001 286 412
AB001425 0 34 37 14 44 51 15 8 0 0 100 117 78 77 84 28 41 33 0 -0.436 -0.184 0.193 0.18 4.642 -0.058 0 12 104 13 33 -10 23 -7 40 446 1407 -0.882 1.148 40 48 30 66 72 34 0.009 11 30
AB001426 1.609 44 67 122 38 46 12 37 30 0 66 81 58 64 67 23 30 17 0 3.05 1.689 0.505 0.587 4.406 3.047 0 80 460 8 45 6 2 28 17 5345 6474 1.692 0.591 181 41 26 72 60 34 0.179 9 47
AB001428 -3.595 2430 2898 2423 38 47 12 100 100 0 29023 27533 23544 66 71 24 100 100 3 0.083 0.105 0.129 0.158 2.65 0.095 0 32 176 31349 30327 2392 28957 2860 27467 92758 881084 234.923 1114.565 83 41 25 85 62 34 0.839 29594 28704
AB001430 0.155 81 185 254 38 48 15 68 59 0 100 190 301 62 69 24 59 40 0 1.114 1.148 0.857 1.072 6.13 1.541 0 32 176 80 275 42 38 147 128 5953 6104 8.647 4.913 137 41 32 157 58 35 0 82 278
AB001431 -2.37 37 70 137 35 43 12 35 28 0 74 213 950 65 76 26 37 20 0 0.193 0.234 0.478 0.573 4.695 0.028 0 80 426 10 181 1 9 34 147 5585 17054 2.154 5.12 196 38 27 445 61 35 0.035 11 175
AB001432 -0.591 82 265 579 37 43 13 66 58 0 129 199 184 62 65 26 83 50 0 0.664 1.661 0.505 0.641 11.453 604.775 0 12 104 111 364 44 67 227 137 3177 2389 16.929 5 218 40 29 92 58 40 0 111 372
AB001434 -0.199 39 48 46 34 50 13 32 17 0 64 97 222 58 71 25 33 16 0 0.871 0.363 0.508 0.565 4.142 0.011 0 80 437 9 52 4 5 14 38 3888 7818 -0.143 1 96 37 25 228 55 35 0.001 10 51
AB001435 -4.705 1375 1449 855 40 44 16 100 100 0 35255 35197 8983 64 67 31 100 100 0 0.038 0.04 0.036 0.033 1.671 0.032 0 12 104 36525 36541 1335 35190 1409 35132 17393 422370 83.611 1130.793 58 43 37 25 60 46 0.592 34281 34306
AB001436 -2.115 61 177 219 37 42 14 66 41 0 174 561 963 69 77 31 100 58 0 0.231 0.285 0.447 0.313 11.914 0.041 0 12 104 128 631 24 104 140 491 2123 6732 9.6 15.586 123 40 32 171 65 40 0.017 124 609
AB001456 2.52 408 813 932 40 45 15 81 78 0 127 625 1012 63 77 29 75 56 0 5.736 1.376 4.319 2.371 7.877 1.219 0 32 176 432 1335 368 64 773 562 26043 20011 48.412 18.286 114 43 34 161 59 38 0.19 455 1354
AB001457 0.385 1366 1502 1136 45 67 18 100 100 0 1070 1595 1504 58 78 26 100 100 0 1.306 0.949 1.307 1.264 2.818 0.413 0 12 104 2331 2993 1320 1011 1457 1536 18039 19140 76.9 56.64 75 49 27 94 55 34 0.156 2359 2995
AB001737 0.232 70 166 266 41 52 14 58 50 0 88 161 214 64 122 25 50 41 0 1.175 1.284 1.442 0.661 7.822 -0.006 0 12 104 52 222 28 24 125 97 1997 1942 7.625 1.542 160 44 28 132 60 21 0.001 54 225
AB001738 -2.246 52 65 50 44 51 19 25 16 0 109 95 55 73 87 35 50 16 0 0.211 0.959 0.461 0.386 2.827 -0.003 0 12 68 42 41 7 35 20 21 782 1137 0.714 0.212 77 48 38 58 69 40 0.003 41 42
AB002663 0.349 126 268 285 37 43 10 87 84 0 141 281 354 71 73 31 62 53 0 1.274 1.102 1.237 1.345 10.089 0.534 0 32 171 157 440 88 69 231 209 8592 9013 21.909 6.69 106 40 23 125 67 42 0.048 160 444
AB003502 -0.931 2114 2799 2805 55 70 24 93 90 0 4009 3627 3769 85 96 38 78 71 0 0.525 0.775 0.975 1.119 3.052 0.738 0 32 161 5983 6285 2059 3924 2744 3541 89594 116062 112.423 91.556 100 59 34 103 80 40 0.707 5869 6246
AB005457 0.075 17023 17236 7089 47 57 21 100 100 0 16202 16820 8776 83 88 33 100 100 0 1.054 1.027 0.938 1.073 1.165 1.08 0 12 104 33095 33926 16976 16119 17189 16737 206842 201849 800.13 503.839 41 51 37 52 78 37 0.836 33233 34038

Total number of rows: 21582

Table truncated, full table size 4125 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap