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Sample GSM483434 Query DataSets for GSM483434
Status Public on Mar 13, 2010
Title MDS patient 138
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 1 (RAEB1)
genome/variation: 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 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 GSM1420495

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 85.20879
1053_at 221.2495
117_at 22.380661
121_at 177.50833
1255_g_at 7.624862
1294_at 417.85712
1316_at 25.592585
1320_at 13.225044
1405_i_at 17.732449
1431_at 14.73343
1438_at 32.415123
1487_at 103.78704
1494_f_at 40.295948
1552256_a_at 174.54553
1552257_a_at 116.09832
1552258_at 31.110075
1552261_at 22.508614
1552263_at 65.97675
1552264_a_at 136.03392
1552266_at 12.5331135

Total number of rows: 54675

Table truncated, full table size 1092 Kbytes.




Supplementary file Size Download File type/resource
GSM483434.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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