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Sample GSM1528447 Query DataSets for GSM1528447
Status Public on Mar 31, 2015
Title 23_20h_BV6
Sample type RNA
Source name mononuclear cells from peripheral blood
Organism Homo sapiens
Characteristics age (years): 67
gender: m
sample source: PB
karyotype: normal
igvh status: unmutated
tp53 mutation: MUT
treatment time: 20h
treatment: BV6
Treatment protocol Primary CLL samples were cultivated using RPMI 1640 (Biochrom AG, Berlin, Germany), supplemented with 10% FCS (Sigma-Aldrich, St. Louis, MO, USA), 2 mM L-Glutamin (Biochrom AG), and Penicillin/Streptomycin (GIBCO, Invitrogen Corporation, Grand Island, NY, USA). Prior to treatment, cells were stained with trypan blue (Sigma-Aldrich), counted, and diluted to a density of 1.0x106 cells/ml. Thawing of viably frozen samples followed the DSMZ (German Collection of microorganisms and cell lines, Braunschweig) guideline. Agents used to treat primary AML sample for 4 and 20 hours in vitro were DMSO (control/carrier; dimethyl sulfoxide; Sigma-Aldrich), and BV6 was synthesized at Genentech, Inc. (South San Francisco, CA, USA).
Extracted molecule total RNA
Extraction protocol The total RNA was purified with a TRIzol-based protocol.
Label Biotin
Label protocol For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
Hybridization protocol Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
Scan protocol Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
Description 23_20h_BV6
Data processing The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
Submission date Oct 20, 2014
Last update date Mar 31, 2015
Contact name Lars Bullinger
Phone +49-30-450-553111
Organization name Charité
Department Hematology, Oncology and Tumorimmunology
Street address Augustenburger Platz 1
City Berlin
ZIP/Postal code 13353
Country Germany
Platform ID GPL570
Series (1)
GSE62533 Inhibitor of apoptosis proteins as promising therapeutic targets in chronic lymphocytic leukemia

Data table header descriptions
VALUE RMA normalized data, log2 transformed

Data table
1007_s_at 9.136058807
1053_at 7.740217686
117_at 5.968468189
121_at 7.833370686
1255_g_at 3.174524069
1294_at 7.401016235
1316_at 7.418978691
1320_at 4.625893593
1405_i_at 7.830626011
1431_at 5.452395439
1438_at 5.76265955
1487_at 7.865064621
1494_f_at 6.17007494
1552256_a_at 6.184431553
1552257_a_at 7.749310017
1552258_at 5.425352097
1552261_at 4.271492958
1552263_at 8.006241798
1552264_a_at 8.420225143
1552266_at 2.879346848

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.

Supplementary file Size Download File type/resource
GSM1528447_K_20h_BV6.CEL.gz 4.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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