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Sample GSM96779 Query DataSets for GSM96779
Status Public on Jun 21, 2006
Title Rat 3 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 3500 7345 140 235 280 25 3 6947 11431 10606.27 736 793 212.83 89.4 86 0 6211 10695 32.64 11362 10126 8017.63 1052 1101 331.38 87.7 77.9 0 10310 9074 34.29 1.66 0.85 0.91 1.63 4.8 0.69 0.84 16521 19769 6947 11431 6211 10695 12639 11264 11469 10094 1.85 0.94 1.01 1.82 0.77 0.88 0.73
2 3885 7330 150 271 280 5 3 8957 11940 9306.11 749 808 222.48 97 95.2 0 8208 11191 40.26 13213 12699 7456.11 1060 1143 400.87 95.9 92.3 0 12153 11639 32.96 1.48 1.04 1.25 1.48 1.42 0.68 0.72 20361 22830 8957 11940 8208 11191 14698 14127 13519 12948 1.65 1.16 1.39 1.65 0.75 0.72 0.57
3 4285 7355 150 218 272 27 3 4328 5049 3621.2 739 794 217.25 84.9 78.4 0 3589 4310 19.92 8794 8789 6169.36 1110 1171 347.57 93.1 80.7 0 7684 7679 25.3 2.14 1.78 1.84 2.27 2.26 1.54 0.81 11273 11989 4328 5049 3589 4310 9783 9777 8548 8542 2.38 1.98 2.05 2.53 1.71 1.25 1.1
4 4675 7330 150 257 280 5 3 3460 4647 3366.53 734 785 207.09 93.4 88.3 0 2726 3913 16.71 9623 9165 6570.06 1089 1161 374.78 93 85.2 0 8534 8076 25.68 3.13 2.06 2.01 2.42 3.61 1.76 0.81 11260 11989 3460 4647 2726 3913 10705 10195 9493 8984 3.48 2.3 2.23 2.69 1.96 1.8 1.65
5 5085 7345 140 238 272 17 3 5433 8107 7584.35 761 808 215.78 85.3 73.5 0 4672 7346 25.18 24485 25838 22473.82 1146 1199 373.29 92.9 82.8 3.4 23339 24692 65.59 5 3.36 3.55 4.66 7.71 2.7 0.83 28011 32038 5433 8107 4672 7346 27238 28743 25963 27468 5.56 3.74 3.95 5.19 3.01 2.47 2.32
6 5480 7335 140 272 280 6 3 4619 8710 8217.12 753 813 252.74 91.9 87.9 0 3866 7957 18.28 21863 25208 17607.46 1224 1281 408.66 97.8 94.1 0.4 20639 23984 53.5 5.34 3.01 4.54 5.68 7.41 1.56 0.53 24505 31941 4619 8710 3866 7957 24321 28042 22959 26680 5.94 3.35 5.05 6.32 1.74 2.57 2.42
7 5885 7345 140 238 272 17 3 6222 9885 9230.14 741 791 208.73 87.4 82.8 0 5481 9144 29.81 21604 20419 16937.06 1168 1218 364.22 91.6 82.4 0 20436 19251 59.32 3.73 2.11 2.19 2.79 5.03 1.61 0.77 25917 28395 6222 9885 5481 9144 24033 22715 22734 21415 4.15 2.34 2.43 3.11 1.8 2.05 1.9
8 6285 7335 160 266 272 8 3 7838 11104 8611.78 794 847 242.25 97.4 95.1 0 7044 10310 32.35 20053 19507 10540.61 1124 1322 546.66 98.1 94.4 0 18929 18383 36.68 2.69 1.78 2.31 2.69 3.07 1.05 0.73 25973 28693 7838 11104 7044 10310 22307 21700 21057 20450 2.99 1.98 2.56 2.99 1.16 1.58 1.43
9 6685 7345 140 217 272 17 3 6911 9519 8532.55 773 802 205.37 88.9 82.9 0 6138 8746 33.65 10897 9839 7091.88 1247 1327 420.47 89.9 75.6 0 9650 8592 25.92 1.57 0.98 1.1 2.27 6.16 0.76 0.83 15788 17338 6911 9519 6138 8746 12122 10945 10735 9558 1.75 1.09 1.22 2.52 0.84 0.81 0.65
10 7080 7335 140 260 280 6 3 6453 9973 8324.84 745 807 221.14 97.7 95.4 0 5708 9228 29.18 9720 9858 5793.87 1339 1392 422.4 96.9 91.5 0 8381 8519 23.01 1.47 0.92 1.09 1.27 0.78 0.63 0.82 14089 17747 6453 9973 5708 9228 10813 10966 9323 9477 1.63 1.03 1.22 1.41 0.7 0.71 0.55
11 3485 7725 150 247 272 5 3 2334 3490 2670.11 727 771 201.86 92.3 84.6 0 1607 2763 11.56 3201 3601 1960.62 1063 1119 337.48 91.9 81.8 0 2138 2538 9.48 1.33 0.92 1.1 1.42 1.42 0.58 0.62 3745 5301 2334 3490 1607 2763 3561 4006 2378 2823 1.48 1.02 1.23 1.57 0.64 0.57 0.41
12 3885 7750 140 228 280 22 3 8410 9038 7323.72 722 793 214.02 93.4 86.8 0 7688 8316 39.29 11924 10680 7637.37 1129 1183 366.5 90.8 80.7 0 10795 9551 32.53 1.4 1.15 1.21 2.01 6.44 0.89 0.73 18483 17867 8410 9038 7688 8316 13265 11881 12009 10625 1.56 1.28 1.34 2.23 0.99 0.64 0.49
13 4275 7735 160 268 272 8 3 7913 9898 6874.56 822 992 592.46 96.3 91 0 7091 9076 13.36 13580 13457 7770.21 1128 1405 864.05 95.9 92.9 0 12452 12329 15.72 1.76 1.36 1.65 1.75 1.02 0.84 0.56 19543 21405 7913 9898 7091 9076 15107 14970 13852 13715 1.95 1.51 1.84 1.95 0.94 0.97 0.81
14 4685 7755 140 225 272 27 3 5526 7936 6863.21 731 795 200.34 88.4 80 0 4795 7205 27.58 6612 7167 5135.63 1124 1179 354.04 90.7 76 0 5488 6043 18.68 1.14 0.84 0.92 1.42 1.75 0.66 0.79 10283 13248 5526 7936 4795 7205 7355 7973 6105 6722 1.27 0.93 1.03 1.58 0.74 0.35 0.19
15 5075 7735 160 263 272 8 3 7462 9532 6492.69 781 950 602.38 94.7 87.8 0 6681 8751 12.39 9399 8885 5200.99 1172 1280 457.05 97.3 93.5 0 8227 7713 20.56 1.23 0.88 0.93 1.25 1.98 0.67 0.7 14908 16464 7462 9532 6681 8751 10456 9884 9152 8580 1.37 0.98 1.04 1.39 0.75 0.45 0.3
16 5485 7755 150 256 272 27 3 6442 9882 9238.42 735 788 197.35 88.3 82.8 0 5707 9147 32.64 30762 28083 24242.23 1156 1220 403.74 95.3 87.1 6.3 29606 26927 76.19 5.19 2.94 2.84 4.59 8.19 2.27 0.75 35313 36074 6442 9882 5707 9147 34220 31240 32934 29954 5.77 3.27 3.16 5.1 2.53 2.53 2.38
17 5880 7725 160 273 280 3 3 8186 11392 8405.73 760 1003 863.77 94.5 89 0 7426 10632 9.48 32412 30600 17825.17 1242 1834 2185.52 96.7 94.1 3.7 31170 29358 14.83 4.2 2.76 3.28 3.6 2.08 1.71 0.65 38596 39990 8186 11392 7426 10632 36056 34040 34674 32659 4.67 3.07 3.65 4 1.9 2.22 2.07
18 6295 7740 140 212 280 18 3 6542 6913 5260.72 774 837 230.65 85.8 81.6 0 5768 6139 28.36 6487 6332 3994.48 1235 1271 365.15 93.9 77.8 0 5252 5097 17.77 0.91 0.83 0.86 2.45 15.51 0.67 0.77 11020 11236 6542 6913 5768 6139 7216 7044 5842 5670 1.01 0.92 0.96 2.72 0.74 0.02 -0.14
19 6680 7730 160 279 268 1 3 6918 7540 4754.32 784 875 335.14 97.1 95.7 0 6134 6756 20.64 7146 7094 3529.86 1320 1376 417.8 98.2 94.6 0 5826 5774 17.1 0.95 0.85 0.9 1.14 1.23 0.6 0.66 11960 12530 6918 7540 6134 6756 7949 7892 6481 6423 1.06 0.95 1.01 1.27 0.67 0.08 -0.07
20 7085 7745 140 220 272 17 3 7298 8150 6216.11 747 807 220.25 85.9 82.3 0 6551 7403 33.13 9511 8182 5282.68 1375 1409 450.43 87.3 73.2 0 8136 6807 21.12 1.24 0.92 0.99 2.12 8.17 0.8 0.89 14687 14210 7298 8150 6551 7403 10580 9102 9051 7572 1.38 1.02 1.1 2.36 0.89 0.47 0.31

Total number of rows: 5760

Table truncated, full table size 1579 Kbytes.




Supplementary data files not provided
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