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Sample GSM866091 Query DataSets for GSM866091
Status Public on Aug 01, 2012
Title Splenic Marginal Zone Lymphoma P68 50XbaI
Sample type genomic
 
Source name Splenic Marginal Zone Lymphoma P68
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 31236.16357
SNP_A-1510136 AB 15618.83643
SNP_A-1511055 BB 23282.91022
SNP_A-1518245 AB 18476.24341
SNP_A-1641749 BB 14880.28027
SNP_A-1641751 BB 24479.84448
SNP_A-1641753 AB 21710.51392
SNP_A-1641755 AA 27998.3822
SNP_A-1641757 BB 19537.10303
SNP_A-1641759 BB 15997.98535
SNP_A-1641761 BB 29275.81641
SNP_A-1641763 AB 19515.6438
SNP_A-1641765 AA 11243.47693
SNP_A-1641767 BB 23514.09015
SNP_A-1641769 AB 34755.80713
SNP_A-1641771 BB 9172.306549
SNP_A-1641773 BB 19991.88611
SNP_A-1641775 BB 12340.51129
SNP_A-1641777 AB 26008.17334
SNP_A-1641779 BB 15184.64075

Total number of rows: 58960

Table truncated, full table size 1663 Kbytes.




Supplementary file Size Download File type/resource
GSM866091.CEL.gz 14.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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