|
| Status |
Public on Dec 31, 2010 |
| Title |
PT1 |
| Sample type |
RNA |
| |
|
| Source name |
PT adherent bone cell
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: prothrombin adherent cells from long bone
strain: Sprague Dawley
|
| Treatment protocol |
Rat bone cells from 2-5 day old Sprague Dawley rats were extracted, as described by Hu et al. Exp Cell Res. 2008; 314: 638-50, in α-Minimum Essential Medium Eagle (α-MEM, Sigma-Aldrich, USA) supplemented with 1 mg/ml BSA and 100 mM HEPES, pH 7.4 (Invitrogen, USA). After the extraction were bone cells adhered to 96-well Nunc MaxiSorp plates (Nunc, Germany), coated with bovine milk OPN or mouse PT.
|
| Growth protocol |
Prothrombin (PT) and osteopontin (OPN) promotes adhesion of different TRAP-positive multinucleated cells isolated from rat long bone (Hu et al. Exp Cell Res. 2008; 314: 638-50).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with the RNeasy plus mini kit (Qiagen, USA)
|
| Label |
biotin
|
| Label protocol |
GeneChip Whole Transcript (WT) sense target labeling assay manual (Affymetrix, USA), version 4 - starting with 300 ng RNA and following the Total RNA labeling protocol to prepare targets for GeneChip gene 1.0 ST Arrays (omitting RiboMinus procedure).
|
| |
|
| Hybridization protocol |
GeneChip® Hybridization, Wash, and Stain Kit (Affymetrix, USA).
|
| Scan protocol |
Arrays were scanned on a GeneChip scanner 3000 7G using default scanner settings. Affymetrix GeneChip® Command Console® (AGCC) was used to process all Affymetrix arrays through fluidics and scanning, and the generation of CEL-files.
|
| Description |
Gene expression data from PT adherent bone cells
|
| Data processing |
Probe set signal values were calculated using GeneChip® Expression Console software using the following methods; Summarization: PLIER, Background Correction: PM-GCBG, Normalization: Global Median.
|
| |
|
| Submission date |
Jan 19, 2010 |
| Last update date |
Dec 31, 2010 |
| Contact name |
Erik Karlström |
| E-mail(s) |
erik.karlstrom@ki.se
|
| Organization name |
Karolinska Institutet
|
| Department |
Department of Laboratory Medicine
|
| Street address |
Division of Pathology
|
| City |
Stockholm |
| ZIP/Postal code |
SE-141 86 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL6247 |
| Series (1) |
| GSE19950 |
Multinucleated Tartrate Resistant Acid Phosphatase Positive Cells with Macrophage and Osteoclast Phenotypes in Bone |
|
