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Sample GSM116321 Query DataSets for GSM116321
Status Public on Sep 30, 2006
Title Mouse neurospheres differentiated in the presence of FGF, A1r corresponds to replicate 3
Sample type RNA
 
Channel 1
Source name FGF-control-a1r
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-a1r
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 1.34 1907 2731 2222 54 84 24 100 100 0 4752 4357 3012 62 89 25 100 100 0 2.532 1.605 1.696 1.293 4.771 2.424 0 12 68 6542 6971 1852 4690 2676 4295 32777 52296 107.259 169.565 81 60 29 69 57 28 0.317 6313 6854
AB000490 0.912 62 86 129 55 109 27 31 17 0 84 199 388 72 80 29 28 17 0 1.881 4.086 1.43 1.348 7.994 63.522 0 80 460 18 157 6 12 31 126 6951 15945 -0.833 4 149 61 25 195 66 36 0.001 18 150
AB001423 0.341 168 293 241 57 73 28 83 83 0 224 399 376 84 88 38 83 75 0 1.267 1.336 1.269 1.689 8.638 0.471 0 12 68 250 550 110 140 235 315 3518 4790 7.774 8.114 82 63 38 94 77 43 0.016 249 546
AB001424 2.167 57 134 183 53 64 26 36 27 0 88 144 195 72 86 28 42 22 0 4.491 0.898 0.684 0.727 7.334 0.859 0 80 416 19 152 3 16 80 72 10719 11588 2.621 2.038 136 59 40 135 66 32 0.134 19 154
AB001425 1.037 69 107 167 63 77 31 32 26 0 115 158 264 102 112 39 37 16 0 2.053 1.247 1.811 1.206 5.125 -8.682 0 80 329 19 99 6 13 44 55 8624 12721 0.943 1.167 155 69 41 166 94 34 0.003 19 100
AB001426 -1.911 65 80 69 57 73 25 32 16 0 83 124 159 80 88 36 32 20 0 0.266 1.916 0.875 0.897 6.513 -12.545 0 80 392 10 65 8 2 22 43 6414 10006 0.286 1 86 63 35 128 74 40 0.002 11 65
AB001428 5.652 865 1192 1150 59 77 29 87 78 0 40586 31628 27416 72 84 28 96 93 3 50.267 27.849 21.392 16.887 4.633 28.984 0 32 170 41318 32688 805 40513 1133 31555 38170 1012103 38.125 1108.654 96 65 37 86 66 33 0.789 37904 30076
AB001430 -1.326 70 141 337 56 68 27 37 17 0 78 134 297 73 78 29 28 17 0 0.399 0.721 0.904 0.869 5.33 -0.046 0 80 358 18 145 13 5 84 61 11308 10792 2.667 1.889 238 62 40 221 67 37 0 20 149
AB001431 -3.439 64 115 184 53 66 25 40 27 0 90 110 102 89 95 38 26 11 0 0.092 0.334 1.198 0.774 7.887 0.143 0 80 328 12 82 11 1 62 20 9229 8837 1.893 0.4 160 58 38 93 82 40 0.028 14 87
AB001432 0 52 78 95 56 66 28 16 15 0 94 128 160 71 85 28 46 27 0 -5.03 2.595 1.352 1.142 5.803 4.595 0 80 368 18 77 -4 22 21 56 6307 10219 0.419 1.5 122 62 42 125 65 33 0.014 16 76
AB001434 -0.74 60 71 55 54 84 28 27 13 0 74 95 96 71 84 28 31 12 0 0.599 1.463 0.608 0.672 6.258 3.806 0 80 388 8 40 5 3 16 24 5713 7613 -0.484 0.385 78 60 33 101 65 33 0.001 9 40
AB001435 5.667 751 1057 1340 55 75 28 100 100 0 35411 35819 12764 73 386 33 100 100 0 50.816 35.692 48.491 54.758 3.117 54.285 0 12 104 36032 36747 695 35337 1001 35746 12690 429837 34.645 1044.484 126 61 37 35 67 8 0.27 33053 33761
AB001436 -0.254 58 90 105 49 63 23 38 28 0 96 98 50 88 99 37 20 6 0 0.838 0.24 1.133 0.933 5.284 0.109 0 80 367 16 50 9 7 41 9 7240 7848 1.115 -0.029 116 54 37 51 81 37 0.007 17 54
AB001456 0.238 920 823 392 56 69 26 91 91 0 1087 1289 1444 68 108 26 83 75 0 1.18 1.592 1.201 0.516 11.723 2.697 0 12 68 1881 1986 863 1018 766 1220 9882 15464 28.448 44.958 47 62 38 112 63 24 0.329 1876 1954
AB001457 0.372 2049 2366 1057 56 128 22 100 100 0 2652 3146 2512 73 88 31 91 91 0 1.295 1.33 1.141 1.02 3.587 1.612 0 12 104 4572 5382 1993 2579 2310 3072 28401 37754 97.96 96.345 44 62 17 79 67 35 0.24 4538 5336
AB001737 0.26 51 98 190 52 62 23 37 22 0 72 108 206 73 80 30 23 17 0 1.198 0.751 0.754 0.59 5.405 0.337 0 80 399 -1 81 0 -1 46 35 7910 8665 1.538 0.893 192 57 38 190 67 37 0.004 -2 83
AB001738 0 53 84 96 60 78 31 26 18 0 90 99 53 84 102 35 28 8 0 -0.898 0.644 0.708 0.668 6.663 2.077 0 80 449 -1 38 -7 6 23 15 6758 7967 0.176 -0.094 115 66 39 53 77 34 0.019 -2 40
AB002663 -1.062 469 773 858 63 71 32 83 75 0 292 408 333 97 105 42 75 66 0 0.479 0.438 0.708 0.605 14.842 1.468 0 12 68 600 1020 406 194 710 310 9278 4903 21.333 7.103 110 69 46 81 89 40 0.023 623 1061
AB003502 0.105 4296 3786 1786 74 83 43 100 100 0 4622 5161 3536 82 98 32 100 100 0 1.075 1.369 1.063 1.328 3.178 1.341 0 12 68 8761 8790 4221 4540 3711 5079 45445 61944 84.438 154.233 47 82 52 68 75 33 0.465 8769 8704
AB005457 0.58 16180 15641 6273 73 96 40 100 100 0 24165 27117 12081 99 133 40 100 100 0 1.495 1.735 1.735 1.712 1.735 1.812 0 12 104 40173 42585 16107 24066 15568 27017 187701 325408 386.614 666.432 40 80 41 44 91 30 0.84 39619 41726

Total number of rows: 21582

Table truncated, full table size 4164 Kbytes.




Supplementary data files not provided
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