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Sample GSM150253 Query DataSets for GSM150253
Status Public on Mar 01, 2007
Title MASMC_WT_PDGF_T15
Sample type RNA
 
Source name MASMC WT 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 15 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 100.5 P 0.002023
AFFX-BioB-M_at 145.4 P 0.000052
AFFX-BioB-3_at 89.5 P 0.000095
AFFX-BioC-5_at 312.7 P 0.000044
AFFX-BioC-3_at 347.1 P 0.000052
AFFX-BioDn-5_at 587.1 P 0.000044
AFFX-BioDn-3_at 1326.1 P 0.000052
AFFX-CreX-5_at 3424.5 P 0.000052
AFFX-CreX-3_at 4824 P 0.000044
AFFX-DapX-5_at 4.6 A 0.239063
AFFX-DapX-M_at 5.2 A 0.60308
AFFX-DapX-3_at 6.8 A 0.783476
AFFX-LysX-5_at 3.7 A 0.529762
AFFX-LysX-M_at 2.5 A 0.834139
AFFX-LysX-3_at 12 P 0.010311
AFFX-PheX-5_at 1.3 A 0.783476
AFFX-PheX-M_at 0.4 A 0.957038
AFFX-PheX-3_at 8.5 A 0.300606
AFFX-ThrX-5_at 3 A 0.724854
AFFX-ThrX-M_at 0.4 A 0.897914

Total number of rows: 45101

Table truncated, full table size 1194 Kbytes.




Supplementary file Size Download File type/resource
GSM150253.CEL.gz 3.7 Mb (ftp)(http) CEL
Raw data provided as supplementary file

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