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Sample GSM387579 Query DataSets for GSM387579
Status Public on Apr 10, 2009
Title DLBCL biopsy, sample 2195
Sample type RNA
 
Source name DLBCL frozen biopsy
Organism Homo sapiens
Characteristics tissue: lymph node tumor
Treatment protocol Not applicable
Growth protocol Lymphoma biopsies were snap frozen in liquid nitrogen or embedded in OCT compound followed by flash freezing in liquid nitrogen
Extracted molecule total RNA
Extraction protocol Tissue samples were homogenized in Trizol and extraction of total RNA was performed according to the manufacturer's instructions.
Label Biotin
Label protocol Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for at least 16 hr at 45C on GeneChip Human Genome Array U133Plus_2. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000A.
Description frozen biopsy of lymph node tumor
Gene expression data from primary DLBCL biopsy
Data processing Data were normalized using MAS5 and subsequently log2 transformed. For Gene Set Enrichment Analysis (GSEA), probesets were first filtered out if mean, mu<50, or coeffient of variation, CV<0.3 (as assessed in 259 B cell-related gene expression profiles from U133Plus_2 arrays) ; these probes do not appear in the attached Matrix.
 
Submission date Mar 30, 2009
Last update date Jan 10, 2023
Contact name Laura Pasqualucci
E-mail(s) [email protected]
Organization name Columbia University
Department Institute for Cancer Genetics
Street address 1130 St Nicholas Avenue
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platform ID GPL570
Series (1)
GSE12195 Mutations of multiple genes deregulate the NF-kB pathway in diffuse large B cell lymphoma

Data table header descriptions
ID_REF
VALUE MAS5 signal intensity, log2 transformed.

Data table
ID_REF VALUE
1007_s_at 6.784
1053_at 9.791
117_at 7.262
121_at 8.277
1255_g_at 5.263
1294_at 8.771
1316_at 5.733
1405_i_at 12.065
1431_at 6.213
1438_at 2.982
1487_at 9.714
1494_f_at 6.721
1552256_a_at 10.602
1552257_a_at 10.552
1552258_at 6.589
1552261_at 2.138
1552263_at 9.134
1552264_a_at 9.822
1552266_at 4.42
1552272_a_at 6.246

Total number of rows: 41334

Table truncated, full table size 681 Kbytes.




Supplementary file Size Download File type/resource
GSM387579.CEL.gz 4.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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