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Sample GSM115542 Query DataSets for GSM115542
Status Public on Jun 22, 2006
Title 7-OHMTX_biological rep1
Sample type RNA
 
Source name ATCC CRL 1582 (lymphoblast)
Organism Homo sapiens
Characteristics male 19 years old
Biomaterial provider ATCC
Treatment protocol MOLT4 cells were exposed to a increased concentrations of 7-OHMTX, until final concentrations of 30000 nM, respectively, were reachedFor this purpose the cells were cultured and sub-cultured bi- weekly in RPMI-1640 medium containing fetal calf serum (10%), penicillin (100 U/ml), streptomycin (100 µg/ml) and L-glutamine (2 mM) and under humidified air containing 5% CO2 and at 37?C. The cultures were tested routinely for contamination by mycoplasma. The cells were cultured in drug-free-medium for at least 3 passages prior to harvesting during logarithmic phase growth (at a density of approximately 0.8-1.5x106/ml) for experimental studies. A Coulter Multi-sizer (Coulter Electronics, Luton, United Kingdom) was used to count the cells.
Extracted molecule total RNA
Extraction protocol RNeasy Midi kit in accordance with manufacturer’s instructions
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip human U133A Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Description Gene expression data from untreated MOLT4 cells
Data processing The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
 
Submission date Jun 21, 2006
Last update date Jun 21, 2006
Contact name Ali Moshfegh
E-mail(s) ali.moshfegh@ki.se
Organization name Karolinska Institutet
Department Oncology and Pathology
Street address Z5:01
City Stockholm
ZIP/Postal code 17176
Country Sweden
 
Platform ID GPL96
Series (1)
GSE5118 Expression data from MOLT4 human cell line

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)

Data table
ID_REF VALUE ABS_CALL
AFFX-BioB-5_at 62.2 P
AFFX-BioB-M_at 46.6 P
AFFX-BioB-3_at 37.9 P
AFFX-BioC-5_at 154.9 P
AFFX-BioC-3_at 140.4 P
AFFX-BioDn-5_at 207.6 P
AFFX-BioDn-3_at 691.4 P
AFFX-CreX-5_at 1580.6 P
AFFX-CreX-3_at 2766.2 P
AFFX-DapX-5_at 1.4 A
AFFX-DapX-M_at 1.3 A
AFFX-DapX-3_at 0.9 A
AFFX-LysX-5_at 3.6 A
AFFX-LysX-M_at 1.8 A
AFFX-LysX-3_at 1.2 A
AFFX-PheX-5_at 1.3 A
AFFX-PheX-M_at 4.3 A
AFFX-PheX-3_at 12.2 A
AFFX-ThrX-5_at 3 A
AFFX-ThrX-M_at 2 A

Total number of rows: 22283

Table truncated, full table size 385 Kbytes.




Supplementary data files not provided

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