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Sample GSM658023 Query DataSets for GSM658023
Status Public on Mar 01, 2011
Title B-CLL PB P254
Sample type RNA
 
Source name B-CLL PB P254
Organism Homo sapiens
Characteristics disease state: B-CLL
tissue: peripheral blood
Growth protocol Peripheral blood from B-CLL patients as well as from healthy donors were firstly separated by Ficoll gradient (GE Healthcare), obtained peripheral mononuclear cells (PBMC). PBMC were shortly incubated in IMDM (Isove’s Modified Dulbecco’s) medium supplemented with 10% fetal calf serum, 1% non essential amino acids, 1% antibiotics. PBMCs from healthy donors were separated by autoMACS Pro Separator and anti FITC microbeads, CD19 human FITC antibody were used.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted by TRIzol Reagent following the manufacturer protocol. Precipitation by isopropyl alcohol (0.5mL per 1mL TRIzol) was done over night. As carrier of the aqueous phase the Acrylamide was used. The RNA pellets were washed with 75% ethanol (1mL per 1mL TRIzol) and dry pellets were resuspend in 20 uL of RNAse free water.
Label biotin
Label protocol RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA were prepared using the recommended Affymetrix reagents and kits.
 
Hybridization protocol RNA was proceeded according to Affymetrix 3‘ – IVT Express Kit protocol. cDNA was hybridized for 16 hr to the Affymetrix array as described in the Expression Analysis Technical Manual. GeneChips were washed and stained in the Affymetrix Fluidics Station.
Scan protocol GeneChips were processed using the Agilent GeneArray Scanner 3000 7G system in the Genomics Facility of the New York University Cancer Institute.
Description Additional information and characteristics in the referred paper supplement xls table.
Data processing Data were summarized using GeneSpring implementation of RMA algorithm and expression data were normalized on median of control samples.
 
Submission date Jan 19, 2011
Last update date Mar 01, 2011
Contact name Vojtěch Kulvait
E-mail(s) vojtech.kulvait@lf1.cuni.cz
Phone +420224965968
Organization name Charles University in Prague - 1st Faculty of Medicine
Department Institute of Pathological Physiology
Lab Centrum for experimental haematology
Street address U Nemocnice 5
City Prague 2
ZIP/Postal code 128 53
Country Czech Republic
 
Platform ID GPL570
Series (1)
GSE26725 Gene expression analysis of 12 B-cell Chronic Lymphocytic Leukemia samples and 5 CD19+ control samples

Data table header descriptions
ID_REF
VALUE RMA algorithm and expression data were normalized on median of control samples

Data table
ID_REF VALUE
AFFX-BioB-5_at -0.9893551
AFFX-BioB-M_at -0.8841257
AFFX-BioB-3_at -0.98038864
AFFX-BioC-5_at -0.97854614
AFFX-BioC-3_at -0.88360786
AFFX-BioDn-5_at -0.8777647
AFFX-BioDn-3_at -0.9573946
AFFX-CreX-5_at -0.4882908
AFFX-CreX-3_at -0.4308014
AFFX-DapX-5_at -0.20376396
AFFX-DapX-M_at -0.22064924
AFFX-DapX-3_at 0.036207438
AFFX-LysX-5_at 0.06790829
AFFX-LysX-M_at 0.08545351
AFFX-LysX-3_at -0.19542861
AFFX-PheX-5_at 0.043466568
AFFX-PheX-M_at -0.22467327
AFFX-PheX-3_at 0.10923338
AFFX-ThrX-5_at -0.10464525
AFFX-ThrX-M_at 0.15171123

Total number of rows: 54675

Table truncated, full table size 1180 Kbytes.




Supplementary file Size Download File type/resource
GSM658023_P254.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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