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Sample GSM658021 Query DataSets for GSM658021
Status Public on Mar 01, 2011
Title B-CLL PB P136
Sample type RNA
 
Source name B-CLL PB P136
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 -0.12707233
AFFX-BioB-M_at -0.14968681
AFFX-BioB-3_at -0.0376482
AFFX-BioC-5_at 0.09841633
AFFX-BioC-3_at 0.19588184
AFFX-BioDn-5_at 0.55968857
AFFX-BioDn-3_at 0.280488
AFFX-CreX-5_at 0.038188934
AFFX-CreX-3_at 0.0021800995
AFFX-DapX-5_at -0.043225765
AFFX-DapX-M_at -0.017576218
AFFX-DapX-3_at -0.1017611
AFFX-LysX-5_at -0.046887636
AFFX-LysX-M_at 0.21310663
AFFX-LysX-3_at -0.093123674
AFFX-PheX-5_at -0.04502368
AFFX-PheX-M_at -0.13019085
AFFX-PheX-3_at 0.4463706
AFFX-ThrX-5_at 0.040387392
AFFX-ThrX-M_at -0.0438962

Total number of rows: 54675

Table truncated, full table size 1176 Kbytes.




Supplementary file Size Download File type/resource
GSM658021_P136.CEL.gz 4.6 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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