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Sample GSM1528456 Query DataSets for GSM1528456
Status Public on Mar 31, 2015
Title 50_4h_D
Sample type RNA
 
Source name mononuclear cells from peripheral blood
Organism Homo sapiens
Characteristics age (years): 70
gender: m
sample source: PB
karyotype: 13q-
igvh status: unmutated
tp53 mutation: WT
treatment time: 4h
treatment: DMSO
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 50_4h_D
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 9.638998985
1053_at 7.997775078
117_at 6.915204048
121_at 7.705532074
1255_g_at 3.142499924
1294_at 6.374063492
1316_at 7.465193272
1320_at 4.666817188
1405_i_at 8.067489624
1431_at 5.151469707
1438_at 5.657793999
1487_at 8.03384304
1494_f_at 6.261343479
1552256_a_at 6.212517262
1552257_a_at 7.332005978
1552258_at 5.690067768
1552261_at 4.430800438
1552263_at 9.341472626
1552264_a_at 9.71349144
1552266_at 2.718591452

Total number of rows: 54675

Table truncated, full table size 1212 Kbytes.




Supplementary file Size Download File type/resource
GSM1528456_W_4h_D.CEL.gz 4.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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