NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM658016 Query DataSets for GSM658016
Status Public on Mar 01, 2011
Title B-CLL PB P138
Sample type RNA
 
Source name B-CLL PB P138
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 0.14341736
AFFX-BioB-M_at 0.011676788
AFFX-BioB-3_at 0.027773857
AFFX-BioC-5_at 0.32855606
AFFX-BioC-3_at 0.35596943
AFFX-BioDn-5_at 0.694294
AFFX-BioDn-3_at 0.51980877
AFFX-CreX-5_at 0.27626514
AFFX-CreX-3_at 0.1961298
AFFX-DapX-5_at -0.06767583
AFFX-DapX-M_at -0.08574104
AFFX-DapX-3_at 0.06798673
AFFX-LysX-5_at 0.072464466
AFFX-LysX-M_at 0.20198321
AFFX-LysX-3_at -0.06667781
AFFX-PheX-5_at -0.035429
AFFX-PheX-M_at -0.078348875
AFFX-PheX-3_at 0.34914875
AFFX-ThrX-5_at -0.020849466
AFFX-ThrX-M_at -0.07141447

Total number of rows: 54675

Table truncated, full table size 1179 Kbytes.




Supplementary file Size Download File type/resource
GSM658016_P138.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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