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| 1 |
GSM96780 |
Rat 4 vehicle-treated in the Nighttime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
 |
pooled |
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). |
| 2 |
GSM96779 |
Rat 3 vehicle-treated in the Nighttime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 3 |
GSM96778 |
Rat 4 EGF-treated in the Nighttime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 4 |
GSM96777 |
Rat 3 EGF-treated in the Nighttime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 5 |
GSM96776 |
Rat 2 vehicle-treated in the Daytime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 6 |
GSM96775 |
Rat 1 vehicle-treated in the Daytime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 7 |
GSM96774 |
Rat 2 EGF-treated in the Daytime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 8 |
GSM96773 |
Rat 1 EGF-treated in the Daytime |
5,760 |
Thomas Jefferson University |
2006-02-14 |
[cDNA Array] TJUDBI Rat 3K (GPL3446) |
RNA |
synthetic construct,Rattus norvegicus
|
pooled |
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). |
| 9 |
GSM947872 |
summer_04-78 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
 |
liver/hepato |
liver, summer active |
| 10 |
GSM947871 |
summer_98-79 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 11 |
GSM947870 |
summer_2000-10 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 12 |
GSM947869 |
summer_20-52 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 13 |
GSM947868 |
summer_20-55 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 14 |
GSM947867 |
summer_2000-2 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 15 |
GSM947866 |
summer_2000-13 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, summer active |
| 16 |
GSM947865 |
late_torpor_04-36 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, hibernating |
| 17 |
GSM947864 |
late_torpor_20-39 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, hibernating |
| 18 |
GSM947863 |
late_torpor_04-06 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, hibernating |
| 19 |
GSM947862 |
late_torpor_04-38 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, hibernating |
| 20 |
GSM947861 |
late_torpor_04-49 |
9,600 |
CAS-MPG partner institute for computational biology |
2012-06-13 |
[cDNA Array] Urocitellus parryii 9.6k (GPL15674) |
RNA |
unidentified
|
liver/hepato |
liver, hibernating |
|
|
|