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Sample GSM96774 Query DataSets for GSM96774
Status Public on Jun 21, 2006
Title Rat 2 EGF-treated in the Daytime
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 3535 7485 140 250 272 23 3 5232 9076 8421.78 751 826 245.87 93.2 89.6 0 4481 8325 21.28 12489 12548 9923.8 1049 1111 344.04 86.8 80.8 0 11440 11499 36.3 2.55 1.38 1.37 1.71 1.24 1.07 0.83 15921 19824 5232 9076 4481 8325 8636 8677 7911 7952 1.77 0.96 0.95 1.18 0.74 0.82 1.35
2 3925 7475 160 264 272 11 3 4979 8144 6903 833 974 444.56 93.2 88.3 0 4146 7311 11.2 16150 15434 8386.73 1201 1481 924.45 97 93.6 0 14949 14233 17.47 3.61 1.95 2.98 3.43 2.79 0.8 0.43 19095 21544 4979 8144 4146 7311 11168 10673 10337 9842 2.49 1.35 2.06 2.37 0.55 1.32 1.85
3 4335 7485 140 222 272 23 3 1687 1800 931.03 780 835 234.8 72.5 64.4 0 907 1020 7.18 6886 6390 4251.53 1039 1099 343.96 93.7 78.4 0 5847 5351 20.02 6.45 5.25 5.43 6.43 10.54 4.1 0.81 6754 6371 1687 1800 907 1020 4762 4419 4043 3700 4.46 3.63 3.76 4.44 2.84 2.16 2.69
4 4725 7470 140 243 280 6 3 1611 1825 893.29 807 849 228.69 78.6 68.3 0 804 1018 7.04 3891 5477 3799.45 1067 1136 384.84 93 80.7 0 2824 4410 10.11 3.51 4.33 3.68 5.74 13.41 3.15 0.55 3628 5428 1611 1825 804 1018 2691 3787 1953 3050 2.43 3 2.55 3.97 2.18 1.28 1.81
5 5135 7475 150 201 272 14 3 3482 4961 3994.7 760 838 248.75 87.6 79.6 0 2722 4201 14 5669 5803 3671.31 1090 1141 329.62 91.5 81.1 0 4579 4713 17.2 1.68 1.12 1.24 1.59 1.46 0.82 0.8 7301 8914 3482 4961 2722 4201 3920 4013 3166 3259 1.16 0.78 0.85 1.1 0.57 0.22 0.75
6 5535 7470 150 257 280 11 3 3458 5583 4598.17 809 866 270.75 93.4 86.8 0 2649 4774 12.77 7176 7688 4373.72 1161 1269 580.62 94.2 89.9 0 6015 6527 12.36 2.27 1.37 2.1 2.32 3.37 0.72 0.57 8664 11301 3458 5583 2649 4774 4962 5316 4159 4513 1.57 0.95 1.45 1.61 0.5 0.65 1.18
7 5935 7475 150 227 272 14 3 3728 5975 5123.87 783 824 228 85 81.1 0 2945 5192 16.35 6342 7422 5489.92 1170 1237 376.25 85.5 75.3 0 5172 6252 16.86 1.76 1.2 1.41 3.17 19.38 0.95 0.78 8117 11444 3728 5975 2945 5192 4386 5132 3576 4323 1.21 0.83 0.97 2.19 0.65 0.28 0.81
8 6325 7475 150 253 272 11 3 4281 6829 5563.01 825 912 357.35 94.5 88.9 0 3456 6004 11.98 6878 7484 3898.28 1288 1501 780.78 93.7 88.9 0 5590 6196 8.81 1.62 1.03 1.39 2.04 4.07 0.61 0.75 9046 12200 4281 6829 3456 6004 4756 5175 3866 4285 1.12 0.71 0.96 1.41 0.42 0.16 0.69
9 6725 7475 150 202 272 11 3 5193 6342 5080.01 793 830 211.92 87.1 84.2 0 4400 5549 24.5 6552 6437 3673.42 1302 1337 426.69 90.6 81.2 0 5250 5135 15.36 1.19 0.93 1.1 1.34 1.19 0.61 0.71 9650 10684 5193 6342 4400 5549 4531 4451 3630 3551 0.83 0.64 0.76 0.93 0.42 -0.28 0.25
10 7125 7475 140 255 272 11 3 3358 6083 5134.93 786 848 276.51 94.1 89.4 0 2572 5297 12.14 5366 5711 3140.51 1290 1377 450.72 92.5 84.7 0 4076 4421 11.91 1.58 0.83 1.09 1.55 3.33 0.48 0.61 6648 9718 3358 6083 2572 5297 3711 3949 2819 3057 1.1 0.58 0.75 1.07 0.33 0.13 0.66
11 3535 7865 160 253 272 9 3 2267 2870 2064.95 777 831 221.62 87.7 77.9 0 1490 2093 10.23 4135 4495 2364.29 1063 1108 354.46 96 88.5 0 3072 3432 11.67 2.06 1.64 1.98 6.86 49.14 0.99 0.75 4562 5525 2267 2870 1490 2093 2859 3108 2124 2373 1.43 1.13 1.37 4.75 0.68 0.51 1.04
12 3925 7875 140 209 272 11 3 4183 5874 4852.69 749 835 269.9 83.7 75.6 0 3434 5125 15.5 11621 9887 7058.28 1087 1123 330.64 93.8 80.4 0 10534 8800 35.15 3.07 1.72 1.81 3.22 5.85 1.26 0.75 13968 13925 4183 5874 3434 5125 8036 6837 7284 6085 2.12 1.19 1.25 2.23 0.87 1.08 1.62
13 4315 7865 140 250 272 10 3 3540 5129 3915.52 777 840 247.45 93.2 89.2 0 2763 4352 14.31 9109 10053 6631.77 1099 1151 356.46 98 91.2 0 8010 8954 25.55 2.9 2.06 2.42 7.87 74.76 1.17 0.48 10773 13306 3540 5129 2763 4352 6299 6952 5539 6192 2 1.42 1.68 5.44 0.81 1 1.54
14 4715 7875 150 209 272 15 3 3975 5114 4043.35 801 855 222.65 86.6 79.4 0 3174 4313 17.85 7017 6854 4486.37 1107 1145 341 90.4 77 0 5910 5747 20.58 1.86 1.33 1.5 3.52 13.03 0.92 0.68 9084 10060 3975 5114 3174 4313 4852 4740 4087 3974 1.29 0.92 1.04 2.43 0.63 0.36 0.9
15 5125 7865 150 258 272 1 3 3229 5413 4263.33 760 827 228.41 92.2 87.6 0 2469 4653 14.14 5510 7186 4281.09 1119 1146 305.36 98.4 92.2 0 4391 6067 18.04 1.78 1.3 1.61 2.18 5.94 0.86 0.74 6860 10720 3229 5413 2469 4653 3810 4969 3036 4195 1.23 0.9 1.12 1.51 0.6 0.3 0.83
16 5525 7875 140 233 272 11 3 3375 5800 5323.77 781 839 274.21 77.3 71.7 0 2594 5019 12.31 11414 12701 10240.44 1155 1206 422.31 91.8 79.8 0 10259 11546 27.03 3.95 2.3 2.58 3.47 4.29 1.68 0.76 12853 16565 3375 5800 2594 5019 7893 8783 7094 7984 2.73 1.59 1.78 2.4 1.16 1.45 1.98
17 5925 7865 150 258 272 1 3 4217 6140 4966.99 770 826 224.37 93.8 90.3 0 3447 5370 18.79 12237 13251 8046.72 1255 1323 388.85 97.7 94.6 0 10982 11996 31.47 3.19 2.23 2.9 3.64 4.55 1.21 0.56 14429 17366 4217 6140 3447 5370 8462 9163 7594 8295 2.2 1.54 2 2.51 0.84 1.14 1.67
18 6335 7865 160 187 272 9 3 957 1053 377.76 772 836 235.86 42.8 24.1 0 185 281 4.06 5108 4709 2154.85 1255 1355 433.38 94.7 78.1 0 3853 3454 11.79 20.83 12.29 16.15 20.43 30.69 4.3 0.57 4038 3735 957 1053 185 281 3532 3256 2664 2388 14.4 8.5 11.17 14.13 2.98 3.85 4.38
19 6715 7855 170 255 272 13 3 1235 1419 608.79 760 830 252.08 70.2 48.2 0 475 659 4.9 6188 5982 2185.78 1353 1419 438.84 98 94.1 0 4835 4629 14.1 10.18 7.02 8.44 13.13 22.34 2.59 0.52 5310 5288 1235 1419 475 659 4279 4137 3343 3201 7.04 4.86 5.83 9.08 1.79 2.82 3.35
20 7135 7875 140 211 272 14 3 5245 5151 3453.75 739 806 232.54 84.8 81 0 4506 4412 22.55 5459 4976 2339.45 1388 1427 452.21 87.2 78.2 0 4071 3588 12.07 0.9 0.81 0.84 2.17 10.74 0.61 0.82 8577 8000 5245 5151 4506 4412 3775 3441 2815 2481 0.62 0.56 0.58 1.5 0.42 -0.68 -0.15

Total number of rows: 5760

Table truncated, full table size 1584 Kbytes.




Supplementary data files not provided
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