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Sample GSM1123466 Query DataSets for GSM1123466
Status Public on Feb 24, 2014
Title Matched Control Group [cv000461 baseline]
Sample type RNA
 
Source name Blood - PaxGene
Organism Homo sapiens
Characteristics group: Matched Control Group
age: 45.57
gender: Female
cad: No
diabetes: No
1 year weight loss (%): 2.86
Treatment protocol Participants were enrolled on an ongoing basis in a lifestyle intervention that consisted of four components: 1) a very low fat vegetarian diet (<10% of calories from fat); 2) 180 minutes/week of moderate aerobic exercise; 3) one hour of stress management each day; and 4) weekly group support sessions (40). Clinical staff met with patients twice each week during the first 12 weeks to orient participants to the program and maximize adherence. The remainder of the program was primarily self-directed but included ongoing weekly stress management and group support sessions.
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Qiagen PAXgene™ Blood RNA System
Label Biotin
Label protocol double-stranded cDNA (1 ug) labeled with biotin-11-UTP using MessageAmp™ II aRNA Amplification System (Ambion)
 
Hybridization protocol Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C onGeneChip® Human Genome U133A 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Scan protocol scanned on a GeneChip® Scanner 3000.
Description Gene Expression Data from a matched Control Group participant
Data processing Partek® Genomics Suite v6.5 (Partek Incorporated) was used to analyze gene expression data from the 378 CEL files, which all passed standard QC assessment. Duplicate blood samples collected at each time point from 7 random participants indicated high repeatability of the microarray data (average Pearson correlation of normalized intensities was 0.992 + 0.006, range 0.969-0.996). Paired t-tests identified 9 genes that were excluded from further analysis because they showed significant differences in expression among duplicate samples based on a false discovery rate (FDR) adjusted P-value <0.05
 
Submission date Apr 16, 2013
Last update date Feb 20, 2015
Contact name Darrell Ellsworth
E-mail(s) d.ellsworth@wriwindber.org
Organization name Windber Research Institute
Street address 620 Seventh St.
City Windber
State/province PA
ZIP/Postal code 15963
Country USA
 
Platform ID GPL571
Series (2)
GSE46097 Expression data of Participants of Ornish intervention and Control group
GSE66175 Imporatance of substantial weight loss for altering gene expression during intensive cardiovascular lifestyle modification

Data table header descriptions
ID_REF
VALUE log2 RMA, standard settings as implemented in Partek

Data table
ID_REF VALUE
1007_s_at 6.48245
1053_at 6.66098
117_at 9.33159
121_at 7.05058
1255_g_at 2.64316
1294_at 8.42805
1316_at 4.80172
1320_at 3.45748
1405_i_at 10.8849
1431_at 3.4353
1438_at 4.21635
1487_at 7.05995
1494_f_at 4.19786
1598_g_at 7.29332
160020_at 6.05537
1729_at 9.03747
1773_at 4.82719
177_at 4.15662
179_at 7.09781
1861_at 6.70145

Total number of rows: 22277

Table truncated, full table size 409 Kbytes.




Supplementary file Size Download File type/resource
GSM1123466_461_Baseline_JW052207.CEL.gz 1.8 Mb (ftp)(http) CEL
GSM1123466_461_Baseline_JW052207MR.CHP.gz 124.2 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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