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Sample GSM658012 Query DataSets for GSM658012
Status Public on Mar 01, 2011
Title Control PB C107
Sample type RNA
 
Source name Control PB C107
Organism Homo sapiens
Characteristics disease state: Control
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.
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 Sep 01, 2016
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
Relations
Reanalyzed by GSE86362

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 -0.0025100708
AFFX-BioB-M_at -0.15423107
AFFX-BioB-3_at -0.17435932
AFFX-BioC-5_at -0.12224388
AFFX-BioC-3_at -0.1334076
AFFX-BioDn-5_at -0.053064346
AFFX-BioDn-3_at -0.09099007
AFFX-CreX-5_at 0.0
AFFX-CreX-3_at 0.0
AFFX-DapX-5_at -0.21499395
AFFX-DapX-M_at -0.16521311
AFFX-DapX-3_at -0.01752019
AFFX-LysX-5_at 0.0
AFFX-LysX-M_at 0.02706623
AFFX-LysX-3_at 0.0
AFFX-PheX-5_at 0.010214806
AFFX-PheX-M_at -0.019926071
AFFX-PheX-3_at -0.16284347
AFFX-ThrX-5_at -0.063043356
AFFX-ThrX-M_at -0.0640285

Total number of rows: 54675

Table truncated, full table size 1107 Kbytes.




Supplementary file Size Download File type/resource
GSM658012_C107.CEL.gz 4.5 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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