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Sample GSM662893 Query DataSets for GSM662893
Status Public on Jul 04, 2011
Title OPM2 DMSO Control
Sample type RNA
 
Source name B lymphocyte
Organism Homo sapiens
Characteristics cell type: Multiple Myeloma Cell Line
cell line: OPM-2
treatment group: DMSO Control
Treatment protocol Cells were treated with 0.5 μmol/L DZNep for 48 h.
Growth protocol Human MM cell lines KMS18, MM.1S and OPM-2 were maintained in RPMI 1640, supplemented with 10% fetal calf serum (FCS), 100 U/mL penicillin and 100 ug/mL streptomycin. MM cell line NCI-H929 was cultured in RPMI 1640 with 15% FCS and 0.00036% 2-mercaptoethanol. All cells were grown at 37°C in a humidified atmosphere with 5% CO2.
Extracted molecule total RNA
Extraction protocol Qiagen RNeasy Mini kit (Germany) extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol Biotinylated aRNA were prepared according to the standard Affymetrix protocol from 100ng total RNA (GeneChip 3' IVT Express Kit Manual, 2009, Affymetrix).
 
Hybridization protocol Following fragmentation, 12.5 ug of aRNA were hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix scanner 3000 7G
Description 7.OPM-2 DMSO
OPM2-DMSO
Data processing The data were analyzed with Genespring GX (Agilent Technologies). The data normalization was done using MAS5 algorithm in GeneSpring GX. For each control-treatment comparison, entities that have flagged present or marginal in at least 1 out of 2 samples were retained, and the differentially expressed genes were identified using the fold change function.
 
Submission date Jan 27, 2011
Last update date Jul 04, 2011
Contact name Zhigang Xie
E-mail(s) xiezhigang@nus.edu.sg
Organization name National University of Singapore
Department CSI Singapore
Street address 14 Medical Drive, CeLS Building #02-07
City Singapore
ZIP/Postal code 117599
Country Singapore
 
Platform ID GPL570
Series (1)
GSE26921 Determinants of sensitivity to DZNep induced apoptosis in multiple myeloma cells

Data table header descriptions
ID_REF
VALUE MAS5 signal
Detection
Detection p-value

Data table
ID_REF VALUE Detection Detection p-value
AFFX-BioB-5_at 569.3 P 0.000509
AFFX-BioB-M_at 699.7 P 0.000044
AFFX-BioB-3_at 478.3 P 0.00006
AFFX-BioC-5_at 1549.9 P 0.000052
AFFX-BioC-3_at 2181.7 P 0.000044
AFFX-BioDn-5_at 3711.5 P 0.000044
AFFX-BioDn-3_at 7976.6 P 0.00007
AFFX-CreX-5_at 21699.5 P 0.000052
AFFX-CreX-3_at 25033.8 P 0.000044
AFFX-DapX-5_at 39.7 P 0.003595
AFFX-DapX-M_at 702 P 0.000662
AFFX-DapX-3_at 2229.9 P 0.000044
AFFX-LysX-5_at 25 A 0.116113
AFFX-LysX-M_at 93.1 P 0.023929
AFFX-LysX-3_at 433.5 P 0.000044
AFFX-PheX-5_at 15.7 A 0.425962
AFFX-PheX-M_at 83.8 P 0.009337
AFFX-PheX-3_at 264.9 P 0.000044
AFFX-ThrX-5_at 4.5 A 0.868639
AFFX-ThrX-M_at 46.7 P 0.030976

Total number of rows: 54675

Table truncated, full table size 1428 Kbytes.




Supplementary file Size Download File type/resource
GSM662893.CEL.gz 4.8 Mb (ftp)(http) CEL
GSM662893.CHP.gz 300.9 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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