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Sample GSM483349 Query DataSets for GSM483349
Status Public on Mar 13, 2010
Title MDS patient 53
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: normal
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 Jun 25, 2014
Contact name Andrea Pellagatti
E-mail(s) andreapellagatti@yahoo.co.uk
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
Relations
Reanalyzed by GSM1420411

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 100.864174
1053_at 178.19382
117_at 26.791616
121_at 316.1965
1255_g_at 9.214099
1294_at 444.9468
1316_at 31.197311
1320_at 14.10172
1405_i_at 13.714151
1431_at 11.1639
1438_at 32.375446
1487_at 118.99124
1494_f_at 36.72457
1552256_a_at 239.28183
1552257_a_at 268.89508
1552258_at 41.23282
1552261_at 24.336958
1552263_at 54.911747
1552264_a_at 114.41677
1552266_at 28.59721

Total number of rows: 54675

Table truncated, full table size 1092 Kbytes.




Supplementary file Size Download File type/resource
GSM483349.CEL.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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