NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM154204 Query DataSets for GSM154204
Status Public on Mar 01, 2007
Title chronic lymphocytic leukemia (CLL 528)
Sample type RNA
 
Source name Bone marrow
Organism Homo sapiens
Characteristics BL from CLL patient, isolated using CD19-PE and CD5-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 BIOTIN
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 08, 2007
Last update date Jan 17, 2007
Contact name Norma Carmen Gutierrez
E-mail(s) normagu@usal.es
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
ID_REF
VALUE RMA NORMALIZED EXPRESSION VALUE

Data table
ID_REF VALUE
1007_s_at 6.482371
1053_at 4.015836
117_at 4.308672
121_at 6.940314
1255_g_at 3.620452
1294_at 7.6922
1316_at 5.219407
1320_at 3.948063
1405_i_at 3.628257
1431_at 3.784579
1438_at 5.289167
1487_at 5.468722
1494_f_at 4.886859
1598_g_at 7.329847
160020_at 6.112618
1729_at 7.053072
1773_at 4.821342
177_at 4.027304
179_at 7.347812
1861_at 4.364538

Total number of rows: 22283

Table truncated, full table size 431 Kbytes.




Supplementary file Size Download File type/resource
GSM154204.CEL.gz 3.4 Mb (ftp)(http) CEL

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap