|
| Status |
Public on Oct 22, 2009 |
| Title |
CCD_ZT0_pool1 |
| Sample type |
RNA |
| |
|
| Source name |
microdissected cortical collecting ducts - ZT0
|
| Organism |
Mus musculus |
| Characteristics |
tissue: left kidney
weight: 25-30g
strain: C57BL/6J
gender: male
|
| 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 |
Male C57BL/6J male mice (Janvier, France) weighing 25-30 g were used in the microarray experiments. The animals were maintained on the standard laboratory chow diet and adapted to 12h-light/12h-dark cycle for two weeks before experiments. During the last three days of the adaptation period, the access to the animal room was forbidden to avoid any interference of the external noise with the animal circadian cycle.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Microdissection of DCT/CNT or CCD was performed from collagenase-treated kidneys. Microarray RNA from microdissected DCT/CNT or CCD was isolated and purified with RNA clean up purification kits from Qiagen. 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 |
For each sample, 10 ng of total RNA were amplified and labeled using the WT-Ovation Pico RNA Amplification System V1, ( NuGen, catalog # 3300-12,) and labeling with FL-Ovation cDNA Biotin Module V2 (NuGen, catalog #4200-12).
|
| |
|
| Hybridization protocol |
The generated cDNAs (5 µg) were fragmented, biotinylated and hybridized using the NuGen FL-Ovation cDNA Biotin Module V2 following the manufacturer’s instructions. The resulting targets were hybridized to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.
|
| Scan protocol |
Scanning was done on an Affymetrix GeneChip Scanner 7G
|
| Description |
CCD_0_r1
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003) for each tissues separately.
|
| |
|
| Submission date |
Aug 20, 2009 |
| Last update date |
Oct 22, 2009 |
| 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 |
GPL1261 |
| Series (1) |
| GSE17739 |
Circadian gene profiling in the distal nephron and collecting ducts |
|
