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Sample GSM1528451 Query DataSets for GSM1528451
Status Public on Mar 31, 2015
Title 44_20h_BV6
Sample type RNA
 
Source name mononuclear cells from peripheral blood
Organism Homo sapiens
Characteristics age (years): 76
gender: m
sample source: PB
karyotype: 13q- bidel
igvh status: mutated
tp53 mutation: WT
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 44_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
E-mail(s) lars.bullinger@charite.de
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
ID_REF
VALUE RMA normalized data, log2 transformed

Data table
ID_REF VALUE
1007_s_at 9.340281487
1053_at 7.154515266
117_at 5.80253458
121_at 8.121166229
1255_g_at 3.141772747
1294_at 7.786919117
1316_at 6.688238621
1320_at 4.795274734
1405_i_at 6.263528347
1431_at 5.073686123
1438_at 5.555749416
1487_at 8.167752266
1494_f_at 6.608590603
1552256_a_at 6.213750362
1552257_a_at 7.355318546
1552258_at 5.540487766
1552261_at 4.428712845
1552263_at 8.229607582
1552264_a_at 8.598104477
1552266_at 2.811347008

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1528451_St_20h_BV6.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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