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Sample GSM154438 Query DataSets for GSM154438
Status Public on Mar 01, 2007
Title normal plasma cells (NPC 625)
Sample type RNA
Source name Bone marrow
Organism Homo sapiens
Characteristics PC from healthy donors, isolated using CD38-APC.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from purified cell
populations using the RNeasy Mini Kit (Qiagen, Valencia, CA,
USA) according to the manufacturer’s instructions. The RNA
integrity was assessed using Agilent 2100 Bioanalyzer (Agilent,
Palo Alto, CA, USA).
Label protocol Labeling were performed according to protocols from Affymetrix.
Briefly,100 ng of total RNA was amplified and labeled using the
GeneChip two-cycle cDNA synthesis kit and GeneChip IVT
labeling kit (Affymetrix Inc., Santa Clara, CA, USA)
Hybridization protocol Hybridizations were performed according to protocols from Affymetrix.
Labeled RNA was hybridized to Human Genome U133A microarray (Affymetrix),
after quality checking on GeneChips Test 3 Arrays.
Scan protocol Washing and scanning were performed using Fluidics Station 400 and
GeneChip Scanner (Affymetrix Inc.).
Description None
Data processing Expression value for each probe set was calculated using
RMAExpress program that uses RMA (robust multi-array
average) algorithm For a first supervised analysis,
gene-filtering methods were applied following the detection
calls calculated using MAS 5.0 algorithm (Affymetrix). Probe sets
with absent calls as well as those showing minimal variation
across all samples (maximum–minimum log2 variation < 2.5)
were filtered out. In a second, more exhaustive analysis, the
complete set of microarrays without gene filtering was
introduced in a multivariable matrix where each of the six cell
states (NBL, WM-BL, CLL-BL, NPC, WM-PC and MM-PC) were
introduced to perform the differential expression analyses.
Submission date Jan 09, 2007
Last update date Jan 17, 2007
Contact name Norma Carmen Gutierrez
Phone 34923291375
Organization name University Hospital
Department Hematology
Street address
City Salamanca
ZIP/Postal code 37007
Country Spain
Platform ID GPL96
Series (1)
GSE6691 Gene expression profiling of B lymphocytes and plasma cells from WaldenstrÖm’s macroglobulinemia.

Data table header descriptions

Data table
1007_s_at 6.092685
1053_at 3.85299
117_at 4.458074
121_at 7.307006
1255_g_at 3.721956
1294_at 7.297343
1316_at 5.319648
1320_at 4.448017
1405_i_at 4.082211
1431_at 4.067505
1438_at 6.019639
1487_at 5.798512
1494_f_at 5.529169
1598_g_at 9.464876
160020_at 6.31617
1729_at 7.200488
1773_at 4.991255
177_at 4.163106
179_at 8.381821
1861_at 4.62628

Total number of rows: 22283

Table truncated, full table size 431 Kbytes.

Supplementary file Size Download File type/resource
GSM154438.CEL.gz 3.6 Mb (ftp)(http) CEL

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