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Sample GSM861797 Query DataSets for GSM861797
Status Public on Aug 01, 2012
Title SMZL_without_7q32del_3
Sample type RNA
 
Source name Splenic Marginal Zone Lymphoma patient sample
Organism Homo sapiens
Characteristics disease state: splenic marginal zone lymphoma
7q32 deletion: no
Growth protocol Mononuclear cells were isolated from peripheral blood of Splenic Marginal Zone Lymphoma patients
Extracted molecule total RNA
Extraction protocol The cells were harvested with TRIzol Reagent (Invitrogen) and the RNA was extracted according to the manufacturer's instructions. As a last step of the extraction procedure, the RNA was purified with the RNeasy Mini-kit (Qiagen, Hilden, Germany).
Label biotin
Label protocol The cDNA was prepared from 2 microg total RNA using the One –Cycle cDNA Synthesis kit from Affymetrix. This cDNA was used for synthezising the cRNA using the IVT labeling kit (Affymetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affymetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133Plus2 chip according to the protocols provided by the manufacturer.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
Description Gene expression data from SMZL patient without 7q32 deletion
Data processing Data were normalized with Bioconductor software using RMA algorithm.
 
Submission date Jan 12, 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 GPL570
Series (2)
GSE35082 INTEGRATIVE ONCOGENOMIC AND HIGH-THROUGHPUT SEQUENCING ANALYSES OF THE COMMONLY DELETED REGION IN CHROMOSOME 7q32 IN SPLENIC MARGINAL ZONE LYMPHOMA (expression)
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 log2 RMA signal

Data table
ID_REF VALUE
1007_s_at 73.75476588
1053_at 81.77271918
117_at 237.8238073
121_at 137.1645089
1255_g_at 5.675593806
1294_at 691.8759595
1316_at 31.85354627
1320_at 14.07868277
1405_i_at 1367.170181
1431_at 12.48668726
1438_at 25.16675463
1487_at 103.831765
1494_f_at 31.74617039
1552256_a_at 116.4147543
1552257_a_at 150.9317999
1552258_at 20.57400681
1552261_at 17.58352323
1552263_at 101.4472483
1552264_a_at 175.9358955
1552266_at 8.683932059

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM861797.CEL.gz 4.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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