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Sample GSM447633 Query DataSets for GSM447633
Status Public on Mar 01, 2010
Title class F, rep24
Sample type RNA
 
Source name Vancouver sample
Organism Homo sapiens
Characteristics tissue type: lymphoma
disease status: chronic Hodgkin lymphoma
relapse type: LATE
age (years): 12
sex: M
disease stage: 2
albumin level: 37
hemoglobin level: 117
lymphocyte percentage: 13
white blood count: 8.78
international prognostic score (ips): 3
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from multiple (10-20x) 20µm freshly cut tissue sections after mechanical homogenization using Allprep RNA extraction kits.
Label biotin
Label protocol 1-8 µg of extracted RNA were used to prepared biotinylated cRNA in a one-cycle reaction following routine protocols including reverse transcription and labeling in-vitro transcription reactions.
 
Hybridization protocol 11µg of labeled cRNA were hybridized on the array overnight. The arrays were washed and stained using Affymetrix Fluidics Station 450.
Scan protocol Arrays were scanned using Affymetrix GeneChip Scanner.
Description VAN_00084f2.CEL
Data processing The data were analyzed with Bioconductor (R), and normalized and summaried using the rma function in the affy package. The quality control thresholds used were present call rates >20% and normalized unscaled standard errors <1.05 (NUSE). Batch-normalization was performed using ComBat.
 
Submission date Sep 01, 2009
Last update date Feb 16, 2010
Contact name Christian Steidl
E-mail(s) csteidl@bccancer.bc.ca
Phone 1-604-675-8046
Organization name BC Cancer Agency
Department Pathology
Lab Steidl lab
Street address 675 West 10th Avenue
City Vancouver
State/province BC
ZIP/Postal code V5Z 1L3
Country Canada
 
Platform ID GPL570
Series (1)
GSE17920 Expression data of diagnostic biopsy samples from Hodgkin lymphoma patients

Data table header descriptions
ID_REF
VALUE log2 rma normalized batch-adjusted signal intensity

Data table
ID_REF VALUE
1007_s_at 4.6059
1053_at 5.7168
117_at 3.1578
121_at 5.8709
1255_g_at 1.7052
1294_at 6.0755
1316_at 2.5737
1320_at 2.2864
1405_i_at 10.6529
1431_at 2.211
1438_at 2.4558
1487_at 4.5625
1494_f_at 3.0237
1552256_a_at 5.966
1552257_a_at 4.5672
1552258_at 3.2593
1552261_at 2.4187
1552263_at 5.357
1552264_a_at 7.4758
1552266_at 2.0188

Total number of rows: 54675

Table truncated, full table size 945 Kbytes.




Supplementary file Size Download File type/resource
GSM447633.CEL.gz 4.0 Mb (ftp)(http) CEL
Processed data included within Sample table

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