|
| Status |
Public on Sep 01, 2007 |
| Title |
II-D |
| Sample type |
RNA |
| |
|
| Source name |
Manually microdissected embryonic tibiae; zone II of growth plate
|
| Organism |
Mus musculus |
| Characteristics |
Tibiae derived from four litters of CD1 mice (Charles River) staged at embryonic day E15.5 were isolated and manually separated into three segments corresponding to early, middle and
late chondrocyte differentiation (Figure 3.1 A, left panel); each litter represented one independent experiment. Starting at either extremity, the region corresponding to approximately the first
third of the bone was segmented and designated zone I, which contains both proliferating and resting cells. Zone II includes segments corresponding to the central region, starting from each
end of the bone and contains mostly prehypertrophic and early hypertrophic chondrocytes. The final zone, zone III, constitutes both the most mature hypertrophic chondrocytes and
the mineralized portion of the tibiae.
|
| Biomaterial provider |
Charles River. Cultures were completed in Frank Beier's laborartory by Lee-Anne Stanton and Hanga Agoston. Data analysis by: Claudine James
|
| Treatment protocol |
No treatment
|
| Growth protocol |
No growth
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiazol lipid tissue extraction kit
|
| Label |
ONE COLOUR: SAPE
|
| Label protocol |
Completed according to the London Regional Genomics Centre (LRGC): http://www.lrgc.ca/
|
| |
|
| Hybridization protocol |
see LRGC specifications
|
| Scan protocol |
see LRGC specifications
|
| Description |
Zone II of growth plate
|
| Data processing |
Microarray data was pre-processed using the GC (guanine and cytosine) Robust Multi-chip Averaging (RMA) algorithm in Genespring GX*.
Expression values were further filtered by retaining only those probe sets with expression values of at least 50 in at least 25% of all conditions, thus generating a list of 22 497 probe sets.
Subsequent zone comparisons from the microdissected tibiae data set (MD) were filtered using a 1.5-fold change threshold that produced lists of 6185, 8134 and 7220 probe sets for the zone I vs. II, II vs. III and zone I vs. III, respectively.
The same data set was also normalized in parallel using RMA using RMAEXPRESS software v.0.4.1 developed by B. Bolstad, University of California, Berkeley (Bolstad et al., 2003).
Background adjustment and quantile normalization parameters were selected for data processing.
|
| |
|
| Submission date |
May 01, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Claudine James |
| E-mail(s) |
claudinegj@hotmail.com, fbeier@uwo.ca
|
| Phone |
(519)661-3387
|
| Fax |
(519)850-2459
|
| Organization name |
University of Western Ontario
|
| Department |
Physiology and Pharmacology
|
| Lab |
Frank Beier/ CIHR Group in Skeletal Development and Remodeling
|
| Street address |
1151 Richmond Street, Suite 2
|
| City |
London |
| State/province |
Ontario |
| ZIP/Postal code |
N6A 5C1 |
| Country |
Canada |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE7685 |
Transcriptional profiling of growth plate chondrocyte differentiation yields insight into endochondral ossification |
|
| Relations |
| Reanalyzed by |
GSE119085 |
