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Sample GSM96778 Query DataSets for GSM96778
Status Public on Jun 21, 2006
Title Rat 4 EGF-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 3495 7545 140 218 272 20 3 8775 14016 12960.12 754 809 221.58 93.6 89 0 8021 13262 39.6 24950 21427 17109.48 1101 1147 337.3 92.7 82.6 0 23849 20326 73.97 2.97 1.53 1.49 1.88 1.22 1.17 0.78 31870 33588 8775 14016 8021 13262 14780 12693 14128 12041 1.76 0.91 0.88 1.11 0.69 0.82 1.57
2 3865 7545 160 266 272 23 3 8937 13813 12079.62 825 1382 1295.57 85.3 75.6 0 8112 12988 6.9 25788 23847 13819.11 1276 2381 2658.61 86.5 82.7 0 24512 22571 9.7 3.02 1.74 2.29 4.3 19.96 1 0.76 32624 35559 8937 13813 8112 12988 15277 14127 14521 13371 1.79 1.03 1.35 2.55 0.59 0.84 1.6
3 4265 7545 140 218 272 23 3 2958 3883 2978.06 770 812 204.46 78.4 69.7 0 2188 3113 14.47 15819 15465 12256.93 1189 1215 381.11 94 84.4 0 14630 14276 41.51 6.69 4.59 4.58 7.34 15.77 3.7 0.81 16818 17389 2958 3883 2188 3113 9371 9161 8667 8457 3.96 2.72 2.71 4.35 2.19 1.99 2.74
4 4675 7535 140 252 272 9 3 2730 3598 2474.4 792 850 256.16 86.9 78.6 0 1938 2806 10.66 9423 13120 10094.2 1232 1305 387.55 98 92.9 0 8191 11888 24.31 4.23 4.24 3.95 4.81 5.28 3.53 0.75 10129 14694 2730 3598 1938 2806 5582 7772 4852 7042 2.5 2.51 2.34 2.85 2.09 1.32 2.08
5 5075 7550 150 239 280 22 3 3474 7914 8358.31 743 791 197.26 79.5 74.9 0 2731 7171 17.61 32692 34017 29262.85 1276 1341 450.39 95 83.7 41.8 31416 32741 72.59 11.5 4.57 4.52 9.68 25.31 2.85 0.66 34147 39912 3474 7914 2731 7171 19366 20151 18611 19395 6.81 2.7 2.68 5.73 1.69 2.77 3.52
6 5485 7530 150 266 280 3 3 4756 8640 7958.73 776 851 313.53 94.4 89.1 0 3980 7864 15.17 46710 40941 24375.98 1451 1712 1164.74 97.7 91 39.8 45259 39490 40.1 11.37 5.02 6.81 8.44 6.36 2.37 0.6 49239 47354 4756 8640 3980 7864 27671 24253 26811 23394 6.74 2.97 4.03 5 1.41 2.75 3.51
7 5895 7545 140 236 272 20 3 4788 9093 9139.87 736 793 216.97 83.9 75 0 4052 8357 22.07 33249 33649 28934.85 1340 1405 453.15 95.3 84.3 34.7 31909 32309 73.37 7.87 3.87 3.94 7.48 17.69 2.66 0.71 35961 40666 4788 9093 4052 8357 19696 19933 18903 19140 4.67 2.29 2.33 4.43 1.57 2.22 2.98
8 6285 7530 150 274 280 3 3 5860 10660 9655.7 792 821 213.53 94.9 93.4 0 5068 9868 27.44 32424 35076 23652.01 1266 1328 379.53 98.5 94.9 17.2 31158 33810 85.43 6.15 3.43 4.17 5.4 4.83 1.85 0.57 36226 43678 5860 10660 5068 9868 19208 20779 18458 20029 3.64 2.03 2.47 3.2 1.09 1.86 2.62
9 6675 7555 140 229 272 27 3 4174 8840 8523.73 722 780 214.74 89.1 82.5 0 3452 8118 19.44 16198 17412 14629.65 1222 1298 387.26 92.6 77.7 0 14976 16190 41.83 4.34 1.99 1.94 4 14.66 1.58 0.84 18428 24308 4174 8840 3452 8118 9596 10315 8872 9591 2.57 1.18 1.15 2.37 0.93 1.36 2.12
10 7075 7530 140 258 280 7 3 5311 8728 7847.07 765 831 249.8 95.7 93.4 0 4546 7963 21.26 14738 16725 11372.75 1311 1372 443.23 95.3 91.9 0 13427 15414 33.25 2.95 1.94 2.38 3.09 4.92 1.26 0.76 17973 23377 5311 8728 4546 7963 8731 9908 7954 9131 1.75 1.15 1.41 1.83 0.75 0.81 1.56
11 3495 7935 150 251 272 14 3 3028 4719 4086.8 765 815 222.74 94 87.6 0 2263 3954 13.59 5668 6875 4769.9 1115 1184 367.18 92.4 85.3 0 4553 5760 15.44 2.01 1.46 1.69 2.4 6.03 0.97 0.69 6816 9714 3028 4719 2263 3954 3358 4073 2697 3412 1.19 0.86 1 1.42 0.57 0.25 1.01
12 3895 7945 130 215 272 20 3 5522 9831 9240.55 737 804 222.13 84.2 79.1 0 4785 9094 24.86 24353 19978 16923.67 1167 1245 407.79 88.4 75.3 0 23186 18811 59.72 4.85 2.07 2.03 3.62 11.07 1.6 0.76 27971 27905 5522 9831 4785 9094 14426 11835 13735 11143 2.87 1.23 1.2 2.14 0.95 1.52 2.28
13 4275 7930 150 265 280 7 3 8839 11435 8654.43 811 1026 723 93.6 89.4 0 8028 10624 12.23 23382 22221 12799.03 1326 1797 1506.79 93.2 90.2 0.8 22056 20895 15.52 2.75 1.97 2.36 4.22 22.33 1.23 0.7 30084 31519 8839 11435 8028 10624 13851 13164 13066 12378 1.63 1.17 1.4 2.5 0.73 0.7 1.46
14 4695 7935 140 201 272 14 3 6234 8665 7356.21 721 779 206.66 87.6 83.6 0 5513 7944 30.17 13802 12459 9101.58 1341 1395 434.08 90.5 77.1 0 12461 11118 31.8 2.26 1.4 1.38 2.76 5.31 1.07 0.74 17974 19062 6234 8665 5513 7944 8176 7381 7382 6586 1.34 0.83 0.82 1.64 0.63 0.42 1.18
15 5090 7925 140 262 280 8 3 6830 10762 7789.87 790 939 489.45 95.4 91.2 0 6040 9972 13.95 11345 12790 7820.94 1392 1496 597.11 96.9 90.5 0 9953 11398 19 1.65 1.14 1.24 1.45 1.87 0.91 0.82 15993 21370 6830 10762 6040 9972 6721 7577 5896 6752 0.98 0.68 0.74 0.86 0.54 -0.03 0.72
16 5475 7945 140 252 272 18 3 3649 9022 9388.57 757 796 217.58 84.5 75.8 0 2892 8265 16.77 27058 34155 29537.03 1301 1315 390.68 96.8 88.9 44 25757 32854 69.26 8.91 3.98 4.27 7.87 17.72 2.63 0.7 28649 41119 3649 9022 2892 8265 16029 20233 15258 19462 5.28 2.35 2.53 4.66 1.56 2.4 3.15
17 5875 7925 160 272 272 8 3 8590 11744 9301.48 806 966 511.01 90.1 87.5 0 7784 10938 16.81 60266 44799 23646.54 1515 2148 2366.9 91.5 88.6 48.2 58751 43284 25.46 7.55 3.96 5.05 8.18 20.4 2.04 0.64 66535 54222 8590 11744 7784 10938 35701 26539 34804 25641 4.47 2.34 2.99 4.85 1.21 2.16 2.92
18 6275 7945 130 209 272 18 3 1398 1496 712.85 737 792 226.39 71.8 60.8 0 661 759 6.18 5557 7765 5980.23 1179 1281 404.43 88.5 71.3 0 4378 6586 13.74 6.62 8.68 8.06 10.04 10.21 6.81 0.66 5039 7345 1398 1496 661 759 3292 4600 2593 3901 3.92 5.14 4.77 5.95 4.03 1.97 2.73
19 6670 7925 160 249 280 12 3 2289 2832 1568.91 797 924 462.86 88.8 71.9 0 1492 2035 4.95 10523 9540 3707.21 1261 1372 486.46 96.4 94.4 0 9262 8279 21.63 6.21 4.07 4.88 5.55 3.54 1.69 0.51 10754 10314 2289 2832 1492 2035 6234 5651 5487 4904 3.68 2.41 2.89 3.29 1 1.88 2.63
20 7075 7925 200 196 272 8 3 5721 8269 6888.58 737 785 199.33 84.7 76.5 0 4984 7532 28.7 16025 12974 9037 1217 1304 401.48 89.8 75.5 0 14808 11757 39.91 2.97 1.56 1.53 2.48 2.89 1.24 0.89 19792 19289 5721 8269 4984 7532 9493 7686 8772 6965 1.76 0.92 0.91 1.47 0.73 0.82 1.57

Total number of rows: 5760

Table truncated, full table size 1590 Kbytes.




Supplementary data files not provided
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