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Sample GSM629990 Query DataSets for GSM629990
Status Public on Jul 10, 2012
Title T_cell
Sample type RNA
 
Source name Purified cells, tonsil, T cells
Organism Homo sapiens
Characteristics tissue: tonsil
cell type: T cells
disease status: healthy control
Growth protocol Frozen biopsies from previously untreated patients for lymphoma samples and purified populations from tonsil or peripheral blood for normal controls.
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 5 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 (Affimetrix). The synthezised cRNA was purified with the GeneChip Sample Cleanup Module (Affimetrix).
 
Hybridization protocol Following fragmentation, 15 microg of cRNA were hybridized to the Affymetrix HG-U133_Plus2 chip according to the protocols provided by the manufacturer.
Scan protocol GeneChips were scanned using the GeneChip Scanner 3000 from Affymetrix.
Data processing RMA (R/Bioconductor processing)
 
Submission date Nov 28, 2010
Last update date Jul 10, 2012
Contact name Victor Segura
E-mail(s) vsegura@unav.es
Organization name FIMA
Department Unit of Proteomics, Genomics and Bioinformatics
Street address Avda. Pío XII, 55
City Pamplona
State/province Navarra
ZIP/Postal code 31008
Country Spain
 
Platform ID GPL570
Series (2)
GSE25638 A mouse model of deregulation of the malt1 oncogene recapitulates the pathogenesis of human malt lymphoma [MALT dataset]
GSE25639 A mouse model of deregulation of the malt1 oncogene recapitulates the pathogenesis of human malt lymphoma

Data table header descriptions
ID_REF
VALUE RMA signal

Data table
ID_REF VALUE
1007_s_at 7.4654333
1053_at 5.694370863
117_at 5.271582068
121_at 8.010571047
1255_g_at 2.803147805
1294_at 8.208735766
1316_at 5.72506016
1320_at 3.756811245
1405_i_at 10.81880389
1431_at 3.169361697
1438_at 4.871018474
1487_at 6.844626753
1494_f_at 5.939664394
1552256_a_at 5.162444415
1552257_a_at 5.931479819
1552258_at 4.523844943
1552261_at 3.239100061
1552263_at 6.210787355
1552264_a_at 6.979650552
1552266_at 2.853362822

Total number of rows: 54675

Table truncated, full table size 1211 Kbytes.




Supplementary file Size Download File type/resource
GSM629990.CEL.gz 4.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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