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Sample GSM96780 Query DataSets for GSM96780
Status Public on Jun 21, 2006
Title Rat 4 vehicle-treated in the Nighttime
Sample type RNA
 
Channel 1
Source name Reference RNA
Organism synthetic construct
Characteristics PCR of vector of empty clone. Hybridizes to all spots evenly.
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Sample RNA
Organism Rattus norvegicus
Characteristics 'Strain:Sprague-Dawley', 'Gender:Male', 'Tissue:Suprachiasmatic Nucleus"
Extracted molecule total RNA
Label Cy5
 
 
Description Adult Sprague-Dawley rats (100-150g) housed individually and entrained to 12:12 light-dark cycles for at least two weeks were rapidly sacrificed between 10:00AM and 12:00PM for daytime treatments and between 4:00 and 6:00 PM for night treatments according to a protocol approved by TJU IACUC. Brains were excised quickly, placed in ice-cold, oxygenated artificial cerebral spinal fluid (ACSF) (10 mM HEPES, pH 7.4, 140 mM NaCl, 5 mM KCl, 1 mM MgCl2, 1 mM CaCl2, 24 mM D-Glucose), and cut into 500 µm coronal sections using a vibroslice vibratome (752M, Camden Instruments, Leica, UK). The resulting SCN slices were cultured in oxygenated ACSF for at least 60 minutes at 35°C. After incubation, slices were bisected along the third ventricle, separating the “left” and “right” SCN, and transferred into a new media containing the treatment (20 nM EGF or vehicle). Slices were incubated in treatment for 60 minutes before taking 0.75 mm micropunches (Stoelting, Chicago, IL). Punches for day treatment were taken at 2 PM (8 hours after lights on) while punches for night treatment were taken at 8PM (2 hrs after lights off). RNA was extracted using the Rneasy mini kit (Qiagen), yielding ~200 nanograms of total RNA/punch. Two hundred to four hundred nanograms total RNA were amplified using two rounds of antisense RNA (aRNA) amplification using the RNA MessageAmp kit (Ambion), yielding no less than 130 µg aRNA. aRNA quality was assessed using Bioanalyzer Picochip (Agilent Technologies, Palo Alto, CA). 2.25 µg of aRNA was used to generate amino-allyl and Cy dye conjugated labeled cDNA (Cy5, Amersham) using the indirect aminoallyl-dNTP approach. Experimental details for hybridization, scanning, and quantification are in the Supporting Information (Materials & Methods) in Zak, Hao, et al (2006).
Data processing log2((ch2 median - ch2 median background)/(ch1 median - ch1 median background))
 
Submission date Feb 14, 2006
Last update date Jun 21, 2006
Contact name Gregory Miller
E-mail(s) miller@che.udel.edu
Organization name Thomas Jefferson University
Department Pathology, Anatomy, and Cell Biology
Lab Daniel Baugh Institute
Street address 1020 Locust Street
City Philadelphia
State/province PA
ZIP/Postal code 19107
Country USA
 
Platform ID GPL3446
Series (1)
GSE4245 EGF treated SCN versus intra-animal control at two circadian times

Data table header descriptions
ID_REF
X X position on the image
Y Y position on the image
Diameter Diameter of spot
F Pixels # signal pixels
B Pixels # background pixels
Footprint Distance from correct grid position
Flags 1 = Good, 3 = Bad or Not Found
Ch1 Median
Ch1 Mean Signal Mean of Reference
Ch1 SD
Ch1 B Median
Ch1 B Mean
Ch1 B SD
Ch1 % > B + 1 SD
Ch1 % > B + 2 SD
Ch1 F % Sat.
Ch1 Median - B
Ch1 Mean - B
Ch1 SignalNoiseRatio
Ch2 Median
Ch2 Mean Signal Mean of Sample
Ch2 SD
Ch2 B Median
Ch2 B Mean
Ch2 B SD
Ch2 % > B + 1 SD
Ch2 % > B + 2 SD
Ch2 F % Sat.
Ch2 Median - B
Ch2 Mean - B
Ch2 SignalNoiseRatio
Ch2 Ratio of Medians Ratio of median intensities, with median background subtracted (Ch2 - Ch2B)/(Ch1 - Ch1B)
Ch2 Ratio of Means
Ch2 Median of Ratios
Ch2 Mean of Ratios
Ch2 Ratios SD
Ch2 Rgn Ratio
Ch2 Rgn R
VALUE same as UNF_VALUE but with flagged values removed
Sum of Medians
Sum of Means
Ch1 N Median
Ch1 N Mean
Ch1 N (Median-B)
Ch1 N (Mean-B)
Ch2 N Median
Ch2 N Mean
Ch2 N (Median-B)
Ch2 N (Mean-B)
Ch2 N Ratio of Medians Normalized Ration of Medians (not used)
Ch2 N Ratio of Means
Ch2 N Median of Ratios
Ch2 N Mean of Ratios
Ch2 N Rgn Ratio
Ch2 N Log Ratio
UNF_VALUE Log2 Ratio of median intensities, background subtracted (not used)

Data table
ID_REF X Y Diameter F Pixels B Pixels Footprint Flags Ch1 Median Ch1 Mean Ch1 SD Ch1 B Median Ch1 B Mean Ch1 B SD Ch1 % > B + 1 SD Ch1 % > B + 2 SD Ch1 F % Sat. Ch1 Median - B Ch1 Mean - B Ch1 SignalNoiseRatio Ch2 Median Ch2 Mean Ch2 SD Ch2 B Median Ch2 B Mean Ch2 B SD Ch2 % > B + 1 SD Ch2 % > B + 2 SD Ch2 F % Sat. Ch2 Median - B Ch2 Mean - B Ch2 SignalNoiseRatio Ch2 Ratio of Medians Ch2 Ratio of Means Ch2 Median of Ratios Ch2 Mean of Ratios Ch2 Ratios SD Ch2 Rgn Ratio Ch2 Rgn R VALUE Sum of Medians Sum of Means Ch1 N Median Ch1 N Mean Ch1 N (Median-B) Ch1 N (Mean-B) Ch2 N Median Ch2 N Mean Ch2 N (Median-B) Ch2 N (Mean-B) Ch2 N Ratio of Medians Ch2 N Ratio of Means Ch2 N Median of Ratios Ch2 N Mean of Ratios Ch2 N Rgn Ratio Ch2 N Log Ratio UNF_VALUE
1 3470 7435 140 232 280 18 3 6454 11193 10524.68 779 826 221.22 93.5 88.4 0 5675 10414 29.17 8153 8116 5751.07 1137 1180 346.23 88.4 77.6 0 7016 6979 23.55 1.24 0.67 0.8 1.04 1.27 0.47 0.75 12691 17393 6454 11193 5675 10414 7864 7828 6767 6731 1.19 0.65 0.77 1 0.45 0.25 0.31
2 3865 7425 150 260 272 7 3 8408 12952 11112.24 764 860 329.92 98.5 94.2 0 7644 12188 25.48 9260 9350 5288.2 1188 1247 396.27 97.3 93.1 0 8072 8162 23.37 1.06 0.67 0.78 1.05 1.18 0.41 0.76 15716 20350 8408 12952 7644 12188 8931 9018 7786 7872 1.02 0.65 0.75 1.02 0.4 0.03 0.08
3 4265 7425 150 202 272 7 3 3638 4174 2802.97 756 819 245.77 83.2 79.2 0 2882 3418 14.8 8716 8313 5860.46 1166 1206 372.53 90.1 78.2 0 7550 7147 23.4 2.62 2.09 2.13 4.13 19.81 1.88 0.81 10432 10565 3638 4174 2882 3418 8407 8018 7282 6893 2.53 2.02 2.05 3.98 1.81 1.34 1.39
4 4665 7430 130 237 280 12 3 2732 3616 2421.48 788 844 253.05 89 84.4 0 1944 2828 10.8 4217 7248 5716.06 1185 1215 344.83 92.4 82.3 0 3032 6063 12.23 1.56 2.14 1.87 2.8 5.04 2.09 0.78 4976 8891 2732 3616 1944 2828 4067 6991 2924 5848 1.5 2.07 1.8 2.7 2.01 0.59 0.64
5 5065 7425 130 245 272 7 3 3053 7121 7302.07 755 803 215.49 83.3 77.1 0 2298 6366 14.17 23531 26245 23123.07 1163 1213 389.6 93.1 82.9 3.3 22368 25082 60.4 9.73 3.94 3.78 7.34 23.52 2.72 0.74 24666 31448 3053 7121 2298 6366 22696 25314 21574 24192 9.39 3.8 3.65 7.08 2.63 3.23 3.28
6 5475 7420 150 259 280 10 3 3922 7319 6679.21 766 841 264.24 95 91.5 0 3156 6553 14.84 19973 28307 21601.61 1186 1353 747.1 98.5 95.8 2.3 18787 27121 26.73 5.95 4.14 4.9 6.87 17.62 2.56 0.62 21943 33674 3922 7319 3156 6553 19264 27302 18120 26158 5.74 3.99 4.72 6.63 2.47 2.52 2.57
7 5865 7435 140 232 272 17 3 4534 8728 8501.26 720 774 218.8 84.5 80.2 0 3814 8008 20.72 17222 17230 14595.31 1178 1207 370.6 91.8 80.2 0 16044 16052 46.47 4.21 2 2.28 3.18 5.03 1.55 0.81 19858 24060 4534 8728 3814 8008 16611 16619 15475 15482 4.06 1.93 2.2 3.07 1.49 2.02 2.07
8 6275 7420 150 254 280 10 3 6711 9804 8203.48 718 787 243.73 96.5 93.3 0 5993 9086 27.53 15955 16456 10277.53 1276 1337 434.46 96.5 93.7 0 14679 15180 36.72 2.45 1.67 1.92 2.84 4.15 1.06 0.71 20672 24266 6711 9804 5993 9086 15389 15872 14158 14641 2.36 1.61 1.85 2.74 1.02 1.24 1.29
9 6670 7425 150 210 280 8 3 5589 8066 6998.24 765 804 228.57 86.7 81.9 0 4824 7301 24.45 7186 7383 4981.41 1224 1273 382.22 90.5 77.1 0 5962 6159 18.8 1.24 0.84 0.98 1.57 2.07 0.6 0.7 10786 13460 5589 8066 4824 7301 6931 7121 5750 5940 1.19 0.81 0.95 1.51 0.58 0.25 0.31
10 7055 7425 130 254 272 12 3 4621 7684 6958.76 753 823 249.64 93.3 91.3 0 3868 6931 18.51 5689 6766 4229.17 1241 1309 399.19 94.1 86.2 0 4448 5525 14.25 1.15 0.8 1.05 1.17 0.85 0.47 0.61 8316 12456 4621 7684 3868 6931 5487 6526 4290 5329 1.11 0.77 1.02 1.13 0.46 0.15 0.2
11 3465 7830 160 231 280 12 3 3163 3960 2843.33 772 822 222.67 91.3 85.3 0 2391 3188 14.2 3266 3474 1818.86 1115 1201 389.62 89.2 77.1 0 2151 2359 8.38 0.9 0.74 0.82 1.15 1.94 0.55 0.74 4542 5547 3163 3960 2391 3188 3150 3351 2075 2275 0.87 0.71 0.79 1.11 0.53 -0.2 -0.15
12 3860 7835 140 205 280 17 3 6918 9292 7820.04 738 789 200.86 90.7 87.3 0 6180 8554 34.44 12679 10461 7740.32 1175 1227 408.65 84.4 75.6 0 11504 9286 31.03 1.86 1.09 1.05 1.49 2.09 0.89 0.8 17684 17840 6918 9292 6180 8554 12229 10090 11096 8956 1.8 1.05 1.01 1.44 0.86 0.84 0.9
13 4255 7825 150 257 272 12 3 6961 9985 7444.14 818 1001 522.39 96.1 93 0 6143 9167 13.33 9691 9992 5517.56 1267 1398 616.99 94.9 90.3 0 8424 8725 15.71 1.37 0.95 1.11 1.19 0.55 0.62 0.7 14567 17892 6961 9985 6143 9167 9347 9637 8125 8415 1.32 0.92 1.07 1.15 0.6 0.4 0.46
14 4665 7835 140 224 272 17 3 6564 8809 7300.04 714 795 230.57 89.7 86.2 0 5850 8095 28.47 5684 5617 3626.13 1154 1192 346.65 86.2 77.2 0 4530 4463 16.4 0.77 0.55 0.6 1.29 3.77 0.42 0.72 10380 12558 6564 8809 5850 8095 5482 5418 4369 4305 0.75 0.53 0.58 1.25 0.41 -0.42 -0.37
15 5060 7820 140 270 268 5 3 6824 9010 6575.34 801 933 436.69 92.6 89.6 0 6023 8209 15.63 4490 5391 3163.32 1167 1241 402.67 94.4 85.9 0 3323 4224 11.15 0.55 0.51 0.55 0.66 0.64 0.42 0.76 9346 12433 6824 9010 6023 8209 4331 5200 3205 4074 0.53 0.5 0.53 0.64 0.4 -0.91 -0.86
16 5465 7845 140 241 272 27 3 6112 9593 9244.78 731 790 205.38 88 81.7 0 5381 8862 29.76 19220 27249 24107.23 1169 1213 368.03 93.4 83 3.3 18051 26080 52.22 3.35 2.94 3 4.68 12.72 2.33 0.8 23432 34942 6112 9593 5381 8862 18538 26282 17410 25154 3.24 2.84 2.9 4.51 2.24 1.69 1.75
17 5865 7820 150 262 280 2 3 7943 10887 8387.05 845 1066 620.4 91.6 86.6 0 7098 10042 12.8 25018 27253 17811.16 1341 1966 1600.46 92.4 90.1 1.1 23677 25912 15.63 3.34 2.58 2.81 10.71 101.22 1.84 0.75 30775 35954 7943 10887 7098 10042 24130 26286 22837 24992 3.22 2.49 2.71 10.33 1.77 1.69 1.74
18 6265 7835 140 192 272 17 3 1405 1441 590.89 729 778 201.51 75.5 64.1 0 676 712 6.97 3706 3743 1691.19 1196 1262 417.47 93.2 75 0 2510 2547 8.88 3.71 3.58 3.72 5.12 8.88 2.21 0.6 3186 3259 1405 1441 676 712 3574 3610 2421 2457 3.58 3.45 3.59 4.94 2.13 1.84 1.89
19 6665 7820 150 256 280 2 3 2284 2684 1361.82 784 957 517.97 89.8 69.5 0 1500 1900 4.41 5914 6704 2957.35 1272 1378 522.53 96.1 91.8 0 4642 5432 11.32 3.09 2.86 3.14 3.22 1.26 1.8 0.69 6142 7332 2284 2684 1500 1900 5704 6466 4477 5239 2.98 2.76 3.03 3.11 1.74 1.58 1.63
20 7065 7830 140 208 280 12 3 6486 7847 6142.74 738 802 228.67 89.4 82.2 0 5748 7109 28.36 6431 6512 3990.21 1264 1310 404.64 89.4 76.4 0 5167 5248 15.89 0.9 0.74 0.8 1.59 6.2 0.59 0.81 10915 12357 6486 7847 5748 7109 6203 6281 4984 5062 0.87 0.71 0.77 1.53 0.56 -0.21 -0.15

Total number of rows: 5760

Table truncated, full table size 1579 Kbytes.




Supplementary data files not provided
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