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Sample GSM150249 Query DataSets for GSM150249
Status Public on Mar 01, 2007
Title MASMC_Hey2_KO_PDGF_T480
Sample type RNA
 
Source name MASMC Hey2 KO cells treated with PDGF
Organism Mus musculus
Characteristics Genetic background: Mixed C57BL/6 and 129SvJ
Passage: 10-20
Treatment protocol Mouse aortic smooth muscle cells were isolated from adventitia stripped, explanted aortas by mincing followed by enzymatic digestion. Cells were plated onto fibronectin coated dishes and cultured in DMEM with serum. Purity was checked by immunostaining for sm alpha actin and calponin.
Growth protocol For PDGF induction, cells were grown to 95% confluency on 150 mm plates, washed 4 times with phosphate-buffered saline, and serum starved with DMEM supplemented with 0.4% FCS. After 48 hours in a 37¡/5% CO2 humidified incubator, the cells were washed four times with phosphate buffered saline and then either treated with DMEM or DMEM supplemented with 5 ng/ml human PDGF-BB. Cells were then incubated in the humidified incubator for 480 minutes.
Extracted molecule total RNA
Extraction protocol After the appropriate length of treatment, the cells were washed one time with phosphate buffered saline and RNA was harvested with the Qiagen RNeasy protocol according to the manufacturerÕs instructions (Qiagen).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
 
Hybridization protocol Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol GeneChips were scanned using the Affymetrix Model 3000 scanner
Description Gene expression data from Hey2 KO and WT MASMCs treated with PDGF for varying amounts of time.
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 Dec 14, 2006
Last update date Aug 28, 2018
Contact name Michael T Chin
E-mail(s) mtchin@u.washington.edu
Organization name University of Washington
Department Medicine
Street address 815 Mercer Street
City Seattle
State/province WA
ZIP/Postal code 98109
Country USA
 
Platform ID GPL1261
Series (1)
GSE6526 Expression time course data HEY2 KO and WT MASMC treated with PDGF
Relations
Reanalyzed by GSE119085

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)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 138.3 P 0.001248
AFFX-BioB-M_at 225.8 P 0.000147
AFFX-BioB-3_at 134.9 P 0.00011
AFFX-BioC-5_at 417.7 P 0.000044
AFFX-BioC-3_at 467.5 P 0.000044
AFFX-BioDn-5_at 864.6 P 0.000044
AFFX-BioDn-3_at 1533 P 0.000044
AFFX-CreX-5_at 4322.6 P 0.000052
AFFX-CreX-3_at 5906.8 P 0.000044
AFFX-DapX-5_at 4.6 A 0.287743
AFFX-DapX-M_at 3.5 A 0.712274
AFFX-DapX-3_at 2.2 A 0.945802
AFFX-LysX-5_at 1.4 A 0.659339
AFFX-LysX-M_at 2.3 A 0.824672
AFFX-LysX-3_at 7.5 M 0.050229
AFFX-PheX-5_at 1.1 A 0.86866
AFFX-PheX-M_at 1.3 A 0.814869
AFFX-PheX-3_at 19.4 A 0.227636
AFFX-ThrX-5_at 5 A 0.48511
AFFX-ThrX-M_at 4 A 0.617401

Total number of rows: 45101

Table truncated, full table size 1194 Kbytes.




Supplementary file Size Download File type/resource
GSM150249.CEL.gz 3.8 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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