|
| Status |
Public on Jan 10, 2015 |
| Title |
pmf 6 |
| Sample type |
RNA |
| |
|
| Source name |
bone marrow mesenchymal stromal cell from patient with primary myelofibrosis
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: primary myelofibrosis
cell type: bone marrow mesenchymal stromal cell
|
| Treatment protocol |
After adhesion cells were amplified during 3 passages in alphaMEM with 10% of FCS. Between each passage cells were trypsinated
|
| Growth protocol |
Mononuclear cells from human bone marrow were separate were separate by Ficoll and cultivated in medium alphaMEM with 10% of FCS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using standard RNA extraction protocols (NucleoSpin RNA II, Macherey-Nagel). RNA samples were quality-checked via the Agilent 2100 Bioanalyzer Platform (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
1µg of total RNA sample was used for linear T7-based amplification. To produce Cy3-labeled cRNA, the RNA samples were amplified and labeled using the Agilent Quick Amp Labeling Kit/Low RNA Input Linear Amp Kit (Agilent Technologies) following manufacturer's protocol.
|
| |
|
| Hybridization protocol |
The hybridization procedure was performed according to the Agilent 60-mer oligo microarray processing protocol using Agilent Gene Expression Hybridization Kit (Agilent Technologies). 1,65µg Cy3-labeled fragmented cRNA in hybridization buffer was hybridized overnight (17 hours, 65°C) to Agilent Whole Human Genome Oligo Microarrays 4x44k using Agilent's recommended hybridization chamber.
|
| Scan protocol |
Fluorescence signals of the hybridized Agilent Microarrays were detected using Agilent's Microarray Scanner System (Agilent Technologies). The Agilent Feature Extraction Software (FES) v9,1 was used to read out and process the microarray image files. The software determines feature intensities including background subtraction.
|
| Description |
primary myelofibrosis
|
| Data processing |
standard Agilent Feature Extraction normalization
|
| |
|
| Submission date |
Feb 20, 2013 |
| Last update date |
Jan 10, 2015 |
| Contact name |
christophe desterke |
| E-mail(s) |
christophe.desterke@inserm.fr
|
| Phone |
+33 (0)145595316
|
| Organization name |
university Paris Sud11
|
| Department |
UFR medecine institute Andre Lwoff
|
| Lab |
hopital Paul Brousse Batiment Lavoisier
|
| Street address |
14-16 avenue Paul Vaillant Couturier
|
| City |
VILLEJUIF |
| ZIP/Postal code |
94807 |
| Country |
France |
| |
|
| Platform ID |
GPL4133 |
| Series (1) |
| GSE44426 |
Transcriptome analysis of bone marrow mesenchymal stromal cells from patients with Primary Myelofibrosis |
|
