|
| Status |
Public on Dec 16, 2013 |
| Title |
Chondrocyte_condensation_6wks_LCM_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Human fetal limb 6 wks
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: 6 wk
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For Condensation and Total Cells samples, LCM was used to place cells in RLT; for 17 wk samples, tissue layers were dissected off the joint surface and put directly in RLT
|
| Label |
biotin
|
| Label protocol |
Affymetrix standard labeling kit
|
| |
|
| Hybridization protocol |
Affymetrix standard hybridization protocol
|
| Scan protocol |
Affymetrix standard scan protocol
|
| Data processing |
The acquisition of each array image was undertaken by using Affymetrix GeneChip Command Console 1.1 (AGCC). Subsequent raw data were analyzed using DNA-Chip Analyzer (D-Chip) with the .CEL files obtained from AGCC. A PM/MM difference model for estimating gene expression levels and a quantile approach for data normalization were used. Thresholds for selecting significant genes were set at a relative difference ≥ 1.5-fold for the experiment involving 5-6 week specimens and ≥ 3.0 fold for experiment involving 17 week specimens, with an absolute difference > 100 signal intensity units. Gene expression that met all three criteria simultaneously was considered as significantly changed. Global functional analyses, network analyses and canonical pathway analyses were performed using Ingenuity Pathway Analysis (Ingenuity® Systems, www.ingenuity.com).
|
| |
|
| Submission date |
Oct 28, 2013 |
| Last update date |
Dec 16, 2013 |
| Contact name |
Denis Evseenko |
| E-mail(s) |
[email protected]
|
| Phone |
323-219-0234
|
| Organization name |
University of Southern California
|
| Department |
Orthopaedic Surgery
|
| Lab |
Evseenko Lab
|
| Street address |
1450 Biggy St
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE51812 |
Identification of chondrocyte subsets during human development |
|
