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Sample GSM866082 Query DataSets for GSM866082
Status Public on Aug 01, 2012
Title Splenic Marginal Zone Lymphoma P22 50XbaI
Sample type genomic
 
Source name Splenic Marginal Zone Lymphoma P22
Organism Homo sapiens
Characteristics tissue: Splenic Marginal Zone Lymphoma
Treatment protocol Not treatment
Growth protocol Cells were cultured in RPMI-1640 medium supplemented with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was extracted from mononuclear cells and cell lines using the Qiagen DNA Mini Kit. DNA quality and quantity was assessed using a Nanodrop Spectrophotometer, PicoGreen and agarose gel electrophoresis.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
 
Hybridization protocol DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.
Scan protocol The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.
Description Hybridized to 50K_Xba
Data processing The CEL files were analyzed using the aroma.affymetrix package of R/Bioconductor (CRLMM-algorithm to produce genotype calls and SNPRMA to produce the summarized signal).
 
Submission date Jan 25, 2012
Last update date Aug 01, 2012
Contact name Vicente Jose Fresquet
E-mail(s) vfresquet@unav.es
Phone 34-948-194700
Fax 34-948-194714
Organization name Center for Applied Medical Research (Cima)
Department Division of Oncology
Lab Molecular Oncology
Street address Av Pio XII 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL2005
Series (2)
GSE35329 INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (SNP data)
GSE35383 INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA

Data table header descriptions
ID_REF
VALUE Genotype Call (SNP call): AA, AB, BB; 'Signal' = Summarized signal
Xba_SIGNAL

Data table
ID_REF VALUE Xba_SIGNAL
SNP_A-1507972 AB 29590.28125
SNP_A-1510136 BB 17152.91461
SNP_A-1511055 BB 26585.52881
SNP_A-1518245 BB 15556.89722
SNP_A-1641749 BB 16233.88
SNP_A-1641751 BB 33909.94727
SNP_A-1641753 BB 33306.43286
SNP_A-1641755 AA 28357.82971
SNP_A-1641757 AB 28161.0918
SNP_A-1641759 BB 31748.96045
SNP_A-1641761 AB 26733.65723
SNP_A-1641763 AA 24724.00836
SNP_A-1641765 AA 7135.268982
SNP_A-1641767 AB 18301.72705
SNP_A-1641769 BB 41035.54712
SNP_A-1641771 BB 10524.32846
SNP_A-1641773 BB 16340.00403
SNP_A-1641775 BB 20407.89368
SNP_A-1641777 AA 31050.04785
SNP_A-1641779 BB 8731.031616

Total number of rows: 58960

Table truncated, full table size 1663 Kbytes.




Supplementary file Size Download File type/resource
GSM866082.CEL.gz 14.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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