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Sample GSM866089 Query DataSets for GSM866089
Status Public on Aug 01, 2012
Title Splenic Marginal Zone Lymphoma P64 50XbaI
Sample type genomic
 
Source name Splenic Marginal Zone Lymphoma P64
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 BB 25531.46875
SNP_A-1510136 BB 18186.48779
SNP_A-1511055 AB 27061.84302
SNP_A-1518245 AB 18870.03247
SNP_A-1641749 BB 13255.37177
SNP_A-1641751 BB 26283.16077
SNP_A-1641753 BB 26121.85364
SNP_A-1641755 AA 32843.29858
SNP_A-1641757 BB 25950.50446
SNP_A-1641759 BB 17658.09753
SNP_A-1641761 BB 27174.2334
SNP_A-1641763 AB 17197.80518
SNP_A-1641765 AA 11064.90839
SNP_A-1641767 AA 22572.91504
SNP_A-1641769 BB 34114.7688
SNP_A-1641771 BB 12186.87442
SNP_A-1641773 BB 17599.30469
SNP_A-1641775 BB 12528.07788
SNP_A-1641777 AB 26180.30615
SNP_A-1641779 BB 11256.66516

Total number of rows: 58960

Table truncated, full table size 1663 Kbytes.




Supplementary file Size Download File type/resource
GSM866089.CEL.gz 13.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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