|
| Status |
Public on Apr 30, 2012 |
| Title |
WT_ZT16_pool2 |
| Sample type |
RNA |
| |
|
| Source name |
whole kidney from wild-type mice, ZT16
|
| Organism |
Mus musculus |
| Characteristics |
tissue: left kidney
genotype/variation: wild type
zt time: 16
|
| Treatment protocol |
Animals were sacrificed for microdissection every 4 hours, i.e. at ZT0, ZT4, ZT8, ZT12, ZT16 and ZT20 (ZT – Zeitgeber (circadian) time, indicates time of light-on as ZT0 and time of light-off as ZT12).
|
| Growth protocol |
A colony of the clock deficient mice was established from breeding pairs of clock(+/-) heterozygous mice originally generated by Debruyne et al. (Neuron, 50: 465-477, 2006). All mice were adapted to a 12 hours light, 12 hours dark cycle (LD) for two weeks and then placed in constant darkness (DD) for 30 hours before sacrifice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from whole kidneys of wild-type or clock deficient mice was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987). All RNA quantities were assessed by NanoDrop-ND-1000 spectrophotometer and the quality of RNA was controlled on Aligent 2100 bioanalyzer chips.
|
| Label |
biotin
|
| Label protocol |
RNA extracted from 2 or 3 mice were combined and 100 ng was used to perform target preparation using the Whole Transcript Sense Target Labeling Protocol procedure (Affymetrix, High Wycombe, UK).
|
| |
|
| Hybridization protocol |
Affymetrix Mouse Gene 1.0 ST arrays were hybridized with 5 microgramme of labeled, amplified cDNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol FS450_0007)
|
| Scan protocol |
Scanning was done on an Affymetrix GeneChip Scanner 7G
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues separately.
|
| |
|
| Submission date |
Feb 16, 2011 |
| Last update date |
Apr 30, 2012 |
| Contact name |
Sylvain Pradervand |
| E-mail(s) |
[email protected]
|
| Phone |
+41 21 692 39 08
|
| Organization name |
UNI Lausanne
|
| Department |
CIG
|
| Lab |
DNA Array Facility
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE27366 |
Mice lacking circadian transcriptional activator Clock exhibit dramatic changes in renal excretory rhythms |
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