|
| Status |
Public on Mar 13, 2010 |
| Title |
MDS patient 111 |
| Sample type |
RNA |
| |
|
| Source name |
Bone marrow CD34+ cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: bone marrow
cell type: CD34+ hematopoietic stem cells (HSC)
disease status: myelodysplastic syndromes (MDS)
disease subtype: refractory anemia with excess blasts 2 (RAEB2)
genome/variation: del5q plus monosomy7/del7q plus other
|
| Treatment protocol |
Mononuclear cells were separated using Histopaque density gradient centrifugation, labelled with CD34 MicroBeads, and then CD34+ cells were isolated using MACS magnetic cell separation columns according to the manufacturer’s recommendations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TRIZOL following the manufacturer’s protocol
|
| Label |
Biotin
|
| Label protocol |
50 ng of total RNA were amplified and biotin-labelled with the Two-Cycle cDNA Synthesis and the Two-Cycle Target Labelling and Control Reagent packages according to the standard Affymetrix protocol.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Human Genome U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using an Affymetrix GeneChip Scanner 3000.
|
| Description |
Gene expression data from bone marrow CD34+ cells
|
| Data processing |
Affymetrix CEL files were pre-processed using Robust MultiChip Analysis (RMA) using GeneSpring 7.3.1.
|
| |
|
| Submission date |
Dec 11, 2009 |
| Last update date |
Mar 13, 2010 |
| Contact name |
Andrea Pellagatti |
| E-mail(s) |
[email protected]
|
| Phone |
00441865222911
|
| Organization name |
University of Oxford
|
| Department |
NDCLS, RDM
|
| Lab |
LLR Molecular Haematology Unit
|
| Street address |
John Radcliffe Hospital
|
| City |
Oxford |
| ZIP/Postal code |
OX3 9DU |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE19429 |
Expression data from bone marrow CD34+ cells of MDS patients and healthy controls |
|
