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Sample GSM121123 Query DataSets for GSM121123
Status Public on Dec 31, 2006
Title 41 A Ptxl 1000/Vehicle/6h/NG
Sample type RNA
 
Channel 1
Source name RNA prepared from 1 day old whole rat pups
Organism Rattus norvegicus
Characteristics 1 day old whole rat pups
Biomaterial provider Rat aortic smooth muscle cells were generated in the Cam Patterson lab
Treatment protocol Untreated rat pups for reference RNA
Growth protocol none
Extracted molecule total RNA
Extraction protocol GITC/Phenol/CHcl3 extraction CsCl2 banding
Label Cyanine-3
Label protocol Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.
 
Channel 2
Source name Rat aortic smooth muscle (tmt: Ptxl 1000/Vehicle/6h/NG)
Organism Rattus norvegicus
Characteristics Cell line: Rat aortic smooth muscle cells (RASMC)
Biomaterial provider Rat aortic smooth muscle cells were generated in the Cam Patterson lab
Treatment protocol Cells were grown in 100 mm dishes in 10% FBS/DMEM to approximately 70-80 % confluence, and were washed once in serum-free DMEM, and then incubated for 16 h in DMEM containing 0.5 % (v/v) FBS. The cells were then stimulated with drug/vehicle, insulin/vehicle in NG/HG for 6/24 hours and were extracted for RNA.
Growth protocol The rat aortic smooth muscle cells were maintained at 37oC (5% CO2) in Dulbecco Minimal Essential Medium supplemented with 10% FBS, 2 mM L-glutamine, 100U/ml penicillin and 100 mg/ml streptomycin.
Extracted molecule total RNA
Extraction protocol The cell monolayer was rinsed twice in cold PBS, 5 ml each. Each plate of cells was then lysed in 0.6 ml of Buffer RLT (RNeasy Mini Kit, Qiagen) and total cellular RNA was prepared following the RNeasy protocol.
Label Cyanine-5
Label protocol Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol.
 
 
Hybridization protocol 2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol.
Scan protocol Slides were washed as indicated in the Agilent protocol. Arrays were then scanned with an Axon GenePix 4000b. Data was obtained using the GenePix Pro 6 software package.
Description Gene expression analysis was conducted using Agilent G4130A Rat 22K microarray slides. Starting with 0.5 ug of total RNA, Cyanine-5 labeled cRNA was produced using the Agilent Low-Input RNA Amplification labeling kit according to manufacturer’s protocol. 2ug sample and 2ug reference amplified cRNAs were fragmented and hybridized to the array for 16 hours in a rotating hybridization oven using the Agilent Target Hybridization Controls and protocol. Slides were washed as indicated in the Agilent protocol. Arrays were then scanned with an Axon GenePix 4000b. Data was obtained using the GenePix Pro 6 software package.
Data processing loess normalization, log2 transformation
 
Submission date Jul 18, 2006
Last update date Jul 28, 2006
Contact name Monte S Willis
E-mail(s) monte_willis@med.unc.edu
Phone 919-843-1938
Fax 919-843-4585
Organization name UNC
Department Pathology & Laboratory Medicine
Lab CCBC
Street address 103 Mason Farm Road
City Chapel Hill
State/province NC
ZIP/Postal code 27759-7525
Country USA
 
Platform ID GPL890
Series (1)
GSE5337 Gene Expression Profiling In Rat Smooth Muscle Cells Modulated by Rapamycin and Paclitaxel.

Data table header descriptions
ID_REF probe IDs from the Agilent G4130
VALUE loess normalization of 2 channels, log2 transformation

Data table
ID_REF VALUE
6712 0.648
13666 -0.372
8434 1.247
5006 0.308
19067 -0.77
10122 -1.205
14308 -0.838
4863 0.306
4628 0.418
12663 0.409
13279 -0.178
1387 -0.419
18100 0.543
12798 -0.083
17773 0.657
2634 0.553
1250 -1.479
18324 0.298
17145 -1.226
6642 -1.314

Total number of rows: 11575

Table truncated, full table size 134 Kbytes.




Supplementary file Size Download File type/resource
GSM121123.gpr.gz 2.5 Mb (ftp)(http) GPR

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