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Sample GSM1035804 Query DataSets for GSM1035804
Status Public on Nov 13, 2012
Title PMO-treated, biological rep4
Sample type RNA
 
Source name 3T3-L1 preadipocytes_PMO-treated
Organism Mus musculus
Characteristics cell type: differentiated 3T3-L1 preadipocytes
treated with: 250 μM Palmitoleic Acid for 48 hrs
sample group: MUFA
Treatment protocol Stocks (25mM) of freshly prepared palmitic acid (PA, 16:0), palmitoleic acid (PMA, 16:1n7), stearic acid (SA, 18:0), and oleic acid (OA, 18:1n9) were dissolved in 100% ethanol (Sigma Aldrich, MO, USA). FA stock solutions were subsequently diluted 1:100 in serum-free maintenance media containing 2% (wt/vol) BSA for a final concentration of 250 µM. Differentiated preadipocytes were treated for 48 hrs with the various FA solutions starting on day 8. The control treatment consisted of cells treated with 2% (wt/vol) BSA and a 1:100 dilution of 100% EtOH for 48 hrs.
Growth protocol 3T3-L1 preadipocytes were seeded at a density of 6.0x10^4 cells per well in six-well plates. Cells were cultured at 37°C in 5% CO2 in basic media consisting of DMEM supplemented with 5% heat-inactivated FBS and 1% penicillin-streptomycin. Differentiation was induced at 2 days post confluence (i.e. day 0) by adding a standard differentiation cocktail consisting of Dex (1 µM), IMBX (0.5 mM), and insulin (5 µg/ml) to basic media. After 2 days the differentiation media was replaced with maintenance media, which consisted of basic media supplemented with only insulin (5 µg/ml). Maintenance media was changed every 2 days for the reminder of the experiment. On day 7 FBS was removed from the media and the duration of the experiment was conducted in serum-free conditions.
Extracted molecule total RNA
Extraction protocol After the treatment period, total RNA was extracted from differentiated preadipocytes using the Qiagen RNeasy Mini Kit (Qiagen, Mississauga, Ontario, Canada) according to the manufacturer’s protocol. Extracted RNA was quantified using a Nanodrop (Fisher Scientific, Waltham, Massachusetts), and stored at -80oC for future analyses. RNA quality was verified using the Agilent 2100 BioAnalyzer (Agilent Technologies Inc., Santa Clara, CA, USA), and only samples with an RNA integrity number (RIN) greater than 9.0 were used for microarray analyses.
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA according to the manufacturer's instructions.
 
Hybridization protocol For each sample, 100 ng of total RNA was prepared for hybridization to Affymetrix Mouse Gene 1.1 ST array strips, according to the manufacturer’s instructions. Strips were then washed and stained on the Affymetrix GeneAtlas platform.
Scan protocol Strips were scanned on the Affymetrix GeneAtlas platform.
Description pma4
Data processing The data was imported into R (version 2.15.0)/Bioconductor (Biobase version 2.16.0) and normalized using the robust multichip average (RMA) implementation in the Affy package (version 1.34.0). Normalized data consists of transcript cluster IDs as identifiers.
 
Submission date Nov 12, 2012
Last update date Nov 13, 2012
Contact name David M Mutch
E-mail(s) dmutch@uoguelph.ca
Phone +1-519-824-4120
Organization name University of Guelph
Department Human Health & Nutritional Sciences
Lab ANNU 308
Street address 50 Stone Road East
City Guelph
State/province Ontario
ZIP/Postal code N1G 2W1
Country Canada
 
Platform ID GPL11533
Series (1)
GSE42220 Gene expression data from differentiated 3T3-L1 preadipocytes treated with Palmitic Acid, Stearic Acid, Palmitoleic Acid, or Oleic Acid

Data table header descriptions
ID_REF
VALUE robust multichip average (RMA) signal

Data table
ID_REF VALUE
10338001 10.48613792
10338002 5.959186824
10338003 8.894091709
10338004 8.519639434
10338005 2.464297752
10338006 2.732705876
10338007 3.11519316
10338008 3.885738136
10338009 7.06176351
10338010 2.46854789
10338011 5.45608196
10338012 2.575879982
10338013 2.276405385
10338014 2.343256327
10338015 2.286338822
10338016 6.685343297
10338017 11.59461258
10338018 6.305182184
10338019 5.089987502
10338020 7.113276938

Total number of rows: 35556

Table truncated, full table size 725 Kbytes.




Supplementary file Size Download File type/resource
GSM1035804_594.ga.cel.gz 4.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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