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Sample GSM96777 Query DataSets for GSM96777
Status Public on Jun 21, 2006
Title Rat 3 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 3515 7340 150 242 280 25 3 7665 12044 11094.29 757 832 269.9 89.3 83.9 0 6908 11287 28.4 12577 11796 9250.49 1172 1245 464.16 83.1 72.7 0 11405 10624 27.1 1.65 0.94 0.9 2.04 12.33 0.7 0.71 18313 21911 7665 12044 6908 11287 9882 9269 8961 8348 1.3 0.74 0.71 1.61 0.55 0.38 0.72
2 3905 7320 150 261 280 9 3 10969 14078 10067.67 905 1203 855.92 94.6 90.8 0 10064 13173 12.82 17096 15689 7720.47 1347 1770 1281.61 95.4 92.7 0 15749 14342 13.34 1.56 1.09 1.3 2.79 14.94 0.61 0.64 25813 27515 10969 14078 10064 13173 13433 12328 12375 11269 1.23 0.86 1.02 2.19 0.48 0.3 0.65
3 4295 7335 160 230 272 11 3 3369 4888 3917.06 778 827 230.47 81.3 74.3 0 2591 4110 14.62 13513 11742 8310.31 1187 1232 375.33 91.7 81.3 0 12326 10555 36 4.76 2.57 2.84 10.31 70.85 1.77 0.7 14917 14665 3369 4888 2591 4110 10618 9226 9685 8294 3.74 2.02 2.23 8.1 1.39 1.9 2.25
4 4695 7330 150 259 280 6 3 3712 4920 3369.4 778 834 232.59 95 87.6 0 2934 4142 15.96 14589 12492 8572.82 1082 1277 378.28 100 95 0 13507 11410 38.57 4.6 2.75 2.72 3.27 3.81 2.27 0.8 16441 15552 3712 4920 2934 4142 11463 9816 10613 8965 3.62 2.16 2.14 2.57 1.78 1.85 2.2
5 5115 7350 140 248 280 33 3 5779 8762 7983.56 781 826 213.82 87.5 79 0 4998 7981 27.03 34632 34616 29062.59 1260 1320 443.47 97.6 88.3 35.9 33372 33356 78.09 6.68 4.18 4.16 5.4 7.8 3.29 0.82 38370 41337 5779 8762 4998 7981 27212 27199 26222 26209 5.25 3.28 3.27 4.25 2.59 2.39 2.74
6 5500 7325 150 265 280 4 3 5477 8831 7697.51 753 822 233.16 94 90.6 0 4724 8078 23.49 40818 39694 24511.29 1341 1446 691.13 96.2 93.6 32.5 39477 38353 59.06 8.36 4.75 5.7 7.3 5.5 2.51 0.62 44201 46431 5477 8831 4724 8078 32073 31190 31019 30136 6.57 3.73 4.48 5.74 1.97 2.72 3.06
7 5915 7350 140 253 280 33 3 6672 10215 9341.59 765 808 209.19 93.3 84.2 0 5907 9450 31.89 34904 30690 25448.4 1295 1328 402.73 96.8 87.4 8.7 33609 29395 86.67 5.69 3.11 2.96 4.77 10.01 2.32 0.72 39516 38845 6672 10215 5907 9450 27426 24115 26408 23097 4.47 2.44 2.32 3.75 1.82 2.16 2.51
8 6300 7325 160 274 280 4 3 7476 10996 9130.14 750 829 243.38 95.6 92.3 0 6726 10246 30.72 37135 34377 20837.57 1250 1300 345.07 99.6 97.4 6.2 35885 33127 107.62 5.34 3.23 4.21 9.34 75.87 1.89 0.68 42611 43373 7476 10996 6726 10246 29179 27012 28197 26030 4.19 2.54 3.3 7.34 1.48 2.07 2.42
9 6695 7325 200 212 272 2 3 7559 9721 8456.77 786 843 240.79 81.6 74.5 0 6773 8935 31.39 15183 12710 9060.81 1260 1326 377.89 94.3 79.2 0 13923 11450 40.18 2.06 1.28 1.33 4.58 14.3 0.93 0.75 20696 20385 7559 9721 6773 8935 11930 9987 10940 8997 1.62 1.01 1.05 3.6 0.73 0.69 1.04
10 7090 7325 160 254 280 6 3 7124 10031 7748.37 858 970 453.22 97.2 94.9 0 6266 9173 15.72 11893 12544 6783.96 1494 1624 631.9 96.9 93.3 0 10399 11050 18.82 1.66 1.2 1.41 1.67 1.06 0.73 0.69 16665 20223 7124 10031 6266 9173 9345 9856 8171 8683 1.3 0.95 1.11 1.31 0.57 0.38 0.73
11 3505 7720 170 259 280 9 3 3815 4788 3608.33 802 843 221.64 91.1 86.9 0 3013 3986 17.21 5250 5742 3313.9 1125 1199 346.96 94.6 89.6 0 4125 4617 15.13 1.37 1.16 1.35 1.68 1.7 0.76 0.69 7138 8603 3815 4788 3013 3986 4125 4512 3241 3628 1.08 0.91 1.06 1.32 0.6 0.11 0.45
12 3900 7750 140 225 268 27 3 8704 9084 7494.61 766 826 235.64 87.1 82.2 0 7938 8318 36.94 17455 14310 10504.21 1209 1235 361.2 94.7 83.6 0 16246 13101 48.32 2.05 1.58 1.72 2.32 2.71 1.25 0.8 24184 21419 8704 9084 7938 8318 13715 11244 12765 10294 1.61 1.24 1.35 1.83 0.98 0.69 1.03
13 4290 7725 160 274 280 6 3 8404 10608 7497.38 839 1032 609.42 92 87.6 0 7565 9769 13.79 17086 16132 8400.29 1236 1563 1067.89 92.7 90.5 0 15850 14896 16 2.1 1.52 1.85 2.47 3.74 0.91 0.66 23415 24665 8404 10608 7565 9769 13425 12676 12454 11705 1.65 1.2 1.45 1.94 0.72 0.72 1.07
14 4685 7715 170 227 272 13 3 6388 8362 6997.57 738 796 208.7 87.7 81.5 0 5650 7624 30.61 8756 8298 5768.38 1191 1232 372.99 90.3 78.9 0 7565 7107 23.47 1.34 0.93 0.99 2.06 5.27 0.76 0.85 13215 14731 6388 8362 5650 7624 6880 6520 5944 5584 1.05 0.73 0.77 1.62 0.6 0.07 0.42
15 5095 7720 150 258 280 3 3 8045 9257 6051.75 781 923 541.16 94.2 88 0 7264 8476 14.87 9918 9948 5428.49 1265 1385 577.74 95 89.5 0 8653 8683 17.17 1.19 1.02 1.1 1.36 1.16 0.78 0.75 15917 17159 8045 9257 7264 8476 7793 7817 6799 6823 0.94 0.8 0.87 1.07 0.61 -0.1 0.25
16 5500 7720 270 73 268 5 1 876 895 253.46 729 796 215.5 32.9 12.3 0 147 166 4.06 1770 1793 246.16 1326 1343 391.53 56.2 9.6 0 444 467 4.52 3.02 2.81 2.83 3.63 4.13 0.72 0.55 1.59 591 633 876 895 147 166 1391 1409 349 367 2.37 2.21 2.23 2.85 0.57 1.25 1.59
17 5900 7725 160 271 280 4 3 10050 12940 9568.85 810 1027 671.51 93.7 87.1 0 9240 12130 14.97 61766 47717 21993.06 1454 2365 2913.39 92.3 91.5 48 60312 46263 21.2 6.53 3.81 4.54 6.09 6.96 1.75 0.58 69552 58393 10050 12940 9240 12130 48533 37494 47390 36351 5.13 3 3.57 4.79 1.38 2.36 2.71
18 6315 7745 150 234 272 29 3 5258 6572 4719.45 765 835 246.53 91.5 84.2 0 4493 5807 21.33 8314 7588 4650.29 1251 1331 397.04 94.4 85 0 7063 6337 20.94 1.57 1.09 1.16 2.15 9.13 0.85 0.75 11556 12144 5258 6572 4493 5807 6533 5962 5550 4979 1.24 0.86 0.91 1.69 0.67 0.3 0.65
19 6695 7720 170 267 280 3 3 8468 9295 5776.39 840 1085 779.93 95.1 90.3 0 7628 8455 10.86 9318 9765 5301.27 1439 1569 597.86 96.6 92.1 0 7879 8326 15.59 1.03 0.98 1.01 1.57 4.59 0.67 0.53 15507 16781 8468 9295 7628 8455 7322 7673 6191 6542 0.81 0.77 0.79 1.23 0.53 -0.3 0.05
20 7105 7745 140 213 272 23 3 9592 9439 7643.07 700 778 199.98 95.3 89.7 0 8892 8739 47.96 8667 8286 7245 1337 1391 418.59 90.1 76.5 0 7330 6949 20.71 0.82 0.8 0.79 1.04 0.86 0.83 0.76 16222 15688 9592 9439 8892 8739 6810 6511 5760 5460 0.65 0.62 0.62 0.82 0.65 -0.63 -0.28

Total number of rows: 5760

Table truncated, full table size 1586 Kbytes.




Supplementary data files not provided
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