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Sample GSM483307 Query DataSets for GSM483307
Status Public on Mar 13, 2010
Title MDS patient 11
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 (RA)
genome/variation: del5q
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 26, 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 GSM1420394

Data table header descriptions
ID_REF
VALUE RMA normalized signal intensity

Data table
ID_REF VALUE
1007_s_at 135.47508
1053_at 410.8531
117_at 31.755472
121_at 231.43161
1255_g_at 8.106109
1294_at 182.93376
1316_at 29.142397
1320_at 16.9928
1405_i_at 195.98788
1431_at 13.300051
1438_at 39.37508
1487_at 82.69508
1494_f_at 39.834824
1552256_a_at 156.91438
1552257_a_at 248.40735
1552258_at 38.348656
1552261_at 20.075253
1552263_at 79.17437
1552264_a_at 115.6767
1552266_at 24.695526

Total number of rows: 54675

Table truncated, full table size 1092 Kbytes.




Supplementary file Size Download File type/resource
GSM483307.CEL.gz 5.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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