NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM96773 Query DataSets for GSM96773
Status Public on Jun 21, 2006
Title Rat 1 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 3475 7390 150 243 280 30 3 5779 10985 11669.8 761 815 223.45 88.1 80.2 0 5018 10224 25.86 18008 19701 16666.77 1107 1140 343.28 93 81.9 0 16901 18594 52.46 3.37 1.82 1.98 3.18 5.91 1.24 0.75 21919 28818 5779 10985 5018 10224 10838 11856 10171 11190 2.03 1.09 1.19 1.91 0.75 1.02 1.75
2 3875 7365 160 271 272 5 3 8821 12422 10091.74 708 1073 684.5 96.7 93 0 8113 11714 12.89 24747 23867 13278.19 1143 1484 1161.47 96.3 94.8 0.4 23604 22724 21.31 2.91 1.94 2.61 2.49 1.03 1.02 0.6 31717 34438 8821 12422 8113 11714 14893 14364 14205 13676 1.75 1.17 1.57 1.5 0.61 0.81 1.54
3 4275 7380 140 221 280 20 3 3159 4275 3359.4 740 790 220.46 80.1 71.5 0 2419 3535 14.33 18851 18616 15302.66 1086 1164 405.39 93.7 78.7 0 17765 17530 46.5 7.34 4.96 4.91 8.36 22.33 4.17 0.84 20184 21065 3159 4275 2419 3535 11345 11203 10691 10550 4.42 2.98 2.96 5.03 2.51 2.14 2.88
4 4665 7365 140 264 272 8 3 3025 4015 2624.52 756 825 252.59 94.7 89 0 2269 3259 11.98 10552 18128 15554.25 1111 1158 363.37 98.5 95.5 0 9441 17017 29.04 4.16 5.22 4.18 4.49 2.37 5.39 0.83 11710 20276 3025 4015 2269 3259 6350 10910 5682 10241 2.5 3.14 2.52 2.7 3.25 1.32 2.06
5 5095 7375 140 244 272 27 3 2971 6968 7656.38 738 789 208.72 79.9 73 0 2233 6230 14.23 41855 35868 29460.81 1094 1150 362.15 97.1 90.6 44.7 40761 34774 115.57 18.25 5.58 6.33 12.28 18.16 2.92 0.57 42994 41004 2971 6968 2233 6230 25189 21586 24531 20928 10.99 3.36 3.81 7.39 1.76 3.46 4.19
6 5475 7355 160 271 272 5 3 4518 8202 7841.6 758 847 289.65 92.6 90.8 0 3760 7444 15.6 56025 44802 22902.46 1225 1681 1716.45 94.8 93.4 46.1 54800 43577 32.64 14.57 5.85 10.56 10.92 7.59 2.06 0.5 58560 51021 4518 8202 3760 7444 33717 26963 32980 26225 8.77 3.52 6.35 6.57 1.24 3.13 3.87
7 5875 7375 140 255 272 15 3 4071 8797 9336.76 704 776 205.99 84.3 74.5 0 3367 8093 19.76 48427 35998 29473.13 1224 1261 362 99.2 93.3 45.5 47203 34774 133.78 14.02 4.3 4.83 23.78 168.26 2.48 0.62 50570 42867 4071 8797 3367 8093 29144 21664 28408 20928 8.44 2.59 2.91 14.31 1.49 3.08 3.81
8 6275 7360 170 277 280 3 3 6237 10688 9649.63 806 901 375.91 93.1 89.2 0 5431 9882 16.59 61487 47500 21540.36 1287 2103 2706.36 94.2 91 47.3 60200 46213 22.72 11.08 4.68 7.27 11.31 23.93 1.53 0.47 65631 56095 6237 10688 5431 9882 37004 28586 36229 27812 6.67 2.81 4.37 6.81 0.92 2.74 3.47
9 6675 7380 130 239 280 20 3 3807 8399 8807.45 708 767 200.16 86.6 79.1 0 3099 7691 19.02 16847 25135 22719.94 1192 1246 397.04 93.7 82.4 2.5 15655 23943 42.43 5.05 3.11 2.86 5.03 6.15 1.94 0.57 18754 31634 3807 8399 3099 7691 10139 15127 9421 14409 3.04 1.87 1.72 3.03 1.17 1.6 2.34
10 7070 7360 140 276 268 1 3 4790 8944 8404.39 771 831 251.74 95.3 92.8 0 4019 8173 19.03 20681 25245 18032.2 1266 1388 626.29 97.5 94.9 0.4 19415 23979 33.02 4.83 2.93 3.78 4.77 7.44 1.58 0.54 23434 32152 4790 8944 4019 8173 12446 15193 11684 14431 2.91 1.77 2.28 2.87 0.95 1.54 2.27
11 3485 7765 150 246 272 13 3 2453 3383 2916.37 723 787 240.32 85 79.7 0 1730 2660 10.21 4310 5463 3944.47 1091 1179 363.53 93.1 82.1 0 3219 4372 11.86 1.86 1.64 1.81 2.27 1.9 1.13 0.7 4949 7032 2453 3383 1730 2660 2594 3288 1937 2631 1.12 0.99 1.09 1.37 0.68 0.16 0.9
12 3875 7785 140 226 272 25 3 4828 8406 7995.1 735 809 225.8 84.5 79.2 0 4093 7671 21.38 28382 24843 20868.82 1065 1143 393.05 95.1 83.2 2.2 27317 23778 72.21 6.67 3.1 2.86 10.61 74.22 2.13 0.66 31410 31449 4828 8406 4093 7671 17081 14951 16440 14310 4.02 1.87 1.72 6.39 1.28 2.01 2.74
13 4265 7765 150 268 272 8 3 6834 9897 7927.8 728 827 267.36 94 91.4 0 6106 9169 25.56 27475 26746 17608.81 1086 1140 362.9 98.9 95.1 2.2 26389 25660 75.71 4.32 2.8 3.1 4.35 6.86 1.88 0.71 32495 34829 6834 9897 6106 9169 16535 16096 15881 15443 2.6 1.68 1.87 2.61 1.13 1.38 2.11
14 4675 7785 150 221 272 25 3 3633 7146 6789.65 738 798 211.38 82.8 73.8 0 2895 6408 17.19 14970 15845 13736.29 1079 1121 299.45 93.7 81.4 0 13891 14766 49.99 4.8 2.3 2.33 5.52 22.21 1.65 0.66 16786 21174 3633 7146 2895 6408 9009 9536 8360 8886 2.89 1.39 1.4 3.32 0.99 1.53 2.26
15 5075 7765 140 252 272 5 3 7934 9756 7227.52 736 803 221.44 97.2 93.3 0 7198 9020 35.83 16359 17164 12156.55 1141 1199 378.69 96.8 92.5 0 15218 16023 43.2 2.11 1.78 1.77 1.97 1.35 1.5 0.8 22416 25043 7934 9756 7198 9020 9845 10330 9158 9643 1.27 1.07 1.06 1.19 0.91 0.35 1.08
16 5465 7775 140 261 272 16 3 3390 8352 9267.59 738 796 215.55 78.5 71.6 0 2652 7614 15.73 37480 35467 29209.22 1112 1194 402.05 98.1 89.7 43.3 36368 34355 93.22 13.71 4.51 6.3 16.93 81.05 2.46 0.61 39020 41969 3390 8352 2652 7614 22556 21345 21887 20675 8.25 2.72 3.79 10.19 1.48 3.04 3.78
17 5875 7760 170 274 280 3 3 7756 11527 9605.55 820 971 548 91.6 87.6 0 6936 10707 14.15 65535 49785 21327.74 1329 2598 3829.15 91.6 90.1 50 64206 48456 17.11 9.26 4.53 6.92 9.92 25.78 1.49 0.45 71142 59163 7756 11527 6936 10707 39440 29961 38640 29162 5.57 2.72 4.16 5.97 0.9 2.48 3.21
18 6275 7780 150 222 280 20 3 5413 7562 6703.86 749 798 214.35 87.8 81.5 0 4664 6813 25.25 9267 9617 7061.86 1178 1233 395.29 91.9 79.3 0 8089 8439 23.44 1.73 1.24 1.42 2.12 4.62 0.96 0.83 12753 15252 5413 7562 4664 6813 5577 5788 4868 5079 1.04 0.75 0.86 1.28 0.58 0.06 0.79
19 6665 7765 160 261 272 8 3 6921 8142 5844.23 769 853 309.28 97.3 96.6 0 6152 7373 22.38 10141 10125 5911.72 1219 1259 381.46 96.9 94.6 0 8922 8906 26.58 1.45 1.21 1.33 1.47 0.83 0.82 0.66 15074 16279 6921 8142 6152 7373 6103 6093 5369 5360 0.87 0.73 0.8 0.88 0.5 -0.2 0.54
20 7075 7770 150 230 280 10 3 5719 7661 6266.89 746 792 204.83 89.1 83 0 4973 6915 27.92 22539 19546 15076.78 1258 1317 417.69 95.7 84.8 0 21281 18288 53.96 4.28 2.64 2.61 4.35 7.71 2.18 0.82 26254 25203 5719 7661 4973 6915 13564 11763 12807 11006 2.58 1.59 1.57 2.62 1.31 1.36 2.1

Total number of rows: 5760

Table truncated, full table size 1583 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap