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Sample GSM116331 Query DataSets for GSM116331
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, b5 corresponds to replicate 7
Sample type RNA
 
Channel 1
Source name FGF-control-b5
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-b5
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 0.493 5468 5535 3438 85 130 56 100 100 0 3913 4698 3669 87 103 49 100 100 0 1.407 1.182 1.148 1.191 2.367 1.031 0 12 104 9208 10059 5383 3825 5449 4610 66415 56388 95.702 92.898 62 86 43 78 87 47 0.422 9224 10069
AB000490 2.821 116 280 547 81 114 51 45 31 0 84 280 933 79 98 36 32 17 0 7.067 0.991 2.131 1.771 9.49 0.205 0 80 458 40 399 35 5 199 200 22423 22459 3.212 5 195 82 44 332 79 36 0.046 41 400
AB001423 -1.55 120 1049 3119 74 104 48 50 33 0 221 1387 3937 84 90 35 66 66 0 0.342 0.748 1.405 0.724 4.074 0.699 0 12 104 182 2277 46 136 974 1303 12585 16655 19.469 36.714 297 75 46 283 84 38 0.795 182 2275
AB001424 -0.818 461 671 571 85 116 47 83 75 0 744 660 500 81 90 36 91 66 0 0.567 1.014 0.342 0.989 7.636 0.133 0 12 68 1039 1164 376 663 586 578 8057 7916 11.667 15.667 85 86 40 75 81 40 0.001 1037 1165
AB001425 1.227 120 167 184 90 136 57 43 27 0 109 118 59 95 111 43 30 13 0 2.341 3.479 2.924 2.456 5.75 62.773 0 80 398 43 99 30 13 77 22 13381 9454 0.534 0.163 110 91 42 50 95 39 0.002 44 100
AB001426 -0.234 233 1042 2448 93 145 63 66 66 0 256 364 343 90 126 40 91 66 0 0.85 3.47 2.142 1.894 9.79 0.15 0 12 104 305 1222 140 165 949 273 12510 4374 14.141 5.9 234 94 43 94 90 32 0 306 1229
AB001428 -3.408 4739 4729 2551 92 159 69 100 100 0 49297 45035 15617 87 238 47 100 100 0 0.094 0.103 0.09 0.095 1.468 0.088 0 12 68 53857 49584 4647 49210 4637 44947 56755 540422 65.9 944.277 53 93 43 34 87 19 0.693 53444 49211
AB001430 -2.086 93 153 202 87 127 58 35 18 0 110 154 174 84 94 38 42 25 0 0.236 0.953 1.472 1.122 6.487 26.234 0 80 390 30 135 5 25 66 69 12281 12349 0.441 1.553 131 88 45 113 84 40 0.002 31 136
AB001431 1.543 153 186 191 59 103 41 58 50 0 111 638 1221 78 89 34 50 41 0 2.914 0.227 1.227 1.3 11.629 0.032 0 12 68 126 686 94 32 126 560 2234 7661 2 16 102 60 40 191 78 38 0.018 127 683
AB001432 0.641 177 289 400 89 123 59 50 50 0 141 186 146 84 139 48 58 33 0 1.56 1.963 5.813 5.33 1.715 0.016 0 12 68 144 301 88 56 200 101 3474 2241 2.783 0.979 138 90 48 78 84 34 0.006 145 303
AB001434 2.497 102 178 275 79 300 55 42 27 0 86 156 303 82 269 39 33 20 0 5.644 1.345 0.888 0.995 4.014 1.695 0 80 395 26 172 22 4 99 73 14249 12496 -2.196 -2.872 154 80 18 194 82 14 0.007 27 173
AB001435 -2.68 5852 6193 4481 57 112 29 91 91 0 37277 35615 9088 78 94 41 100 100 0 0.156 0.173 0.144 0.099 5.518 0.119 0 12 104 42992 41673 5794 37198 6136 35537 74321 427388 204.6 858.317 72 58 26 25 78 43 0.449 42702 41401
AB001436 -0.349 87 108 94 71 131 46 33 22 0 99 179 363 79 89 36 33 23 0 0.785 0.377 1.406 1.586 5.756 -0.032 0 80 418 35 136 15 20 37 99 8756 14371 -0.489 2.472 86 72 35 202 79 40 0 36 137
AB001456 -0.044 3035 3820 3443 75 177 55 100 100 0 3119 3407 2800 66 85 29 100 100 0 0.97 1.121 0.981 1.239 3.148 1.168 0 12 104 6013 7085 2960 3053 3744 3341 45846 40893 65.661 113.483 90 76 31 82 66 34 0.383 6013 7090
AB001457 0.921 4998 5039 2063 94 131 65 100 100 0 2670 2964 1890 80 141 42 100 100 0 1.893 1.715 1.817 1.983 2.348 1.652 0 12 68 7494 7828 4904 2590 4945 2883 60476 35573 75.061 66.595 40 95 49 63 80 30 0.414 7516 7849
AB001737 -1.698 128 210 264 92 142 53 33 25 0 210 353 519 91 100 41 83 66 0 0.308 0.451 1.068 1.237 5.211 0.005 0 12 104 155 378 36 119 117 261 2518 4240 1.259 6.098 125 93 37 147 91 41 0 155 378
AB001738 0 74 122 132 94 143 64 30 18 0 114 139 165 104 127 50 25 10 0 -2.181 0.837 2.061 1.867 4.083 2.48 0 80 463 -10 62 -19 9 28 34 9833 11113 -0.323 0.24 108 95 44 118 104 39 0.001 -11 63
AB002663 1.346 1543 2155 1905 111 152 65 100 100 0 648 1062 1191 84 94 38 91 91 0 2.542 2.09 2.29 1.785 3.675 3.287 0 12 104 1994 3021 1431 563 2043 978 25867 12755 30.636 25.237 88 113 42 112 84 40 0.13 2003 3032
AB003502 0.622 18998 15410 8038 110 178 67 100 100 0 12381 13976 9782 110 196 50 100 100 0 1.539 1.103 1.283 1.141 1.801 0.993 0 12 104 31158 29165 18887 12271 15299 13866 184931 167718 226.103 273.04 52 112 37 69 109 25 0.653 31223 29181
AB005457 -0.034 14339 19054 16896 118 297 77 96 93 0 14681 17704 17670 116 139 60 87 84 0 0.977 1.077 1.206 2.159 4.576 1.012 0 32 170 28785 36523 14220 14565 18935 17588 609731 566548 242.731 290.033 88 120 26 99 115 43 0.828 28784 36538

Total number of rows: 21582

Table truncated, full table size 4317 Kbytes.




Supplementary data files not provided
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