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Sample GSM2330004 Query DataSets for GSM2330004
Status Public on Sep 28, 2017
Title SubjectID 89, low MC-SFA, after
Sample type RNA
 
Source name subcutaneous adipose tissue, low MC-SFA, after
Organism Homo sapiens
Characteristics gender: male
individual: 89
diet_group: low MC-SFA + casein
tissue: subcutaneous adipose tissue
metabolic syndrome: n
age: 69
weight: 78
height: 173.5
waisttohipratio: 0.99
Treatment protocol This study is a secondary analysis of a randomized, parallel-controlled, double-blinded, 12-wk diet intervention study that was designed to examine the effects of milk fat, with a high or low MC-SFA content, and of milk protein, whey or casein, on post-prandial lipemia. Design and methods of the original study were described in detail previously (Bohl et al. 2015, doi: 10.3945/ajcn.114.097923). Briefly, 52 participants were randomized in a 2 × 2 factorial design to one of 4 diets: high MC-SFA + casein, low MC-SFA + casein, high MC-SFA + whey, and low MC-SFA + whey. In this paper, we examine the effects of MC-SFAs on whole genome gene expression in subcutaneous adipose tissue in a subpopulation of 12 subjects, 6 in the high MC-SFA + casein group and 6 in the low MC-SFA + casein groups.
Growth protocol Participants needed to be ≥18 y of age, have an abdominal circumference of ≥80 cm for women or ≥94 cm for men, and be weight stabile for at least 3 months prior to inclusion. Furthermore, they could not be diabetic, pregnant, lactating, or suffer from severe cardiovascular, renal, endocrine, or psychiatric disease. All participants gave written informed consent to participate in the study and the study protocol was approved by the Central Denmark Region Committees on Health Research Ethics. The study was registered at clinicaltrials.gov as NCT01472666.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using RNeasy micro kit from Qiagen. RNA integrity was checked on chip analysis (Agilent 2100 bioanalyzer, Agilent Technologies, Amsterdam, the Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 7.0).
Label biotin
Label protocol One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT expression kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).
 
Hybridization protocol Hybridization and washing of the Affymetrix GeneChip Human Gene 1.1 ST arrays were performed on a GeneTitan Instrument (Affymetrix, Santa Clara, CA) according to the manufacturer's recommendations.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Description G144_B05_89_m2t0_mn3
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2).
 
Submission date Sep 27, 2016
Last update date Sep 28, 2017
Contact name Juri C Matualatupauw
E-mail(s) jurimatualatupauw@gmail.com
Organization name Wageningen University
Department Human Nutrition
Street address PO Box 17
City Wageningen
ZIP/Postal code 6700 AA
Country Netherlands
 
Platform ID GPL11532
Series (1)
GSE87382 Dietary medium-chain saturated fatty acids induce gene expression of energy metabolism-related pathways in adipose tissue of abdominally obese subjects

Data table header descriptions
ID_REF
VALUE RMA signal (as log2)

Data table
ID_REF VALUE
7892501 3.361267958
7892502 3.752556883
7892503 3.871810231
7892504 6.92437777
7892505 2.277637473
7892506 2.26147298
7892507 5.547348153
7892508 6.212966093
7892509 9.063998554
7892510 4.706157173
7892511 3.357839314
7892512 4.759181274
7892513 2.845880554
7892514 8.984639814
7892515 8.013407038
7892516 2.292411576
7892517 5.256967083
7892518 2.536956539
7892519 2.652335118
7892520 8.103879942

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2330004_G144_B05_89_m2t0_mn3.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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