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Sample GSM2236501 Query DataSets for GSM2236501
Status Public on Apr 25, 2018
Title placebo_b; 213JJ
Sample type RNA
 
Source name Peripheral blood mononuclear cells, placebo treatment, before intervention, subject 213
Organism Homo sapiens
Characteristics treatment: placebo
subjectid: 213
before/after supplementation: before
Treatment protocol The study was a randomized, double blind, placebo-controlled, cross-over trial in which subjects received two 4-week interventions; epicatechin (100mg/day) or placebo (microcrystalline cellulose). Details of the study have been previously described (Dower et al., 2015; PMID: 25934864). In brief, subjects received both interventions in random order with a wash-out period of 4-week between both interventions. Subjects consumed 2 capsules per day with a glass of water: one during breakfast and one during dinner. Subjects were asked to avoid consumption of epicatechin-rich foods throughout the study. Fasting peripheral blood mononuclear cells (PBMC) were collected before (T0) and after each intervention period (T4) using BD Vacutainer Cell Preparation Tubes. On the day prior to each study day, subjects received a standardized evening meal, refrained from alcohol consumption and strenuous exercise, and were not allowed to eat or drink anything except water after 10.00 pm.
Growth protocol Apparently healthy men and women aged 40–80 y were recruited from Wageningen and surroundings, in The Netherlands. Eligible for participation were nonsmoking men and women, with a BMI (in kg/m2) between 20 and 40 and systolic blood pressure (SBP) between 125 and 160 mm Hg on 2 separate occasions. Exclusion criteria included the presence of diabetes mellitus; cardiovascular, gastrointestinal, or liver disease; usage of antihypertensive or cholesterol-lowering medication or corticosteroids; adherence to a prescribed diet; unstable weight in the past 2 mo; ≥10 h/wk moderate to vigorous physical activity (≥3 metabolic equivalent tasks); and pregnancy or lactation. All subjects gave written informed consent for participation in this study, which was reviewed and approved by the local Medical Ethical Committee of Wageningen University. All procedures were executed according to the declaration of Helsinki. This study was registered at clinicaltrials.gov as NCT01691404.
Extracted molecule total RNA
Extraction protocol RNA was isolated (RNeasy Micro kit, Qiagen, Venlo, the Netherlands), quantified (Nanodrop ND 1000, Nanodrop technologies, Wilmington, Delaware USA) and integrity was checked by an Agilent 2100 Bioanalyser with RNA 6000 microchips (Agilent Technologies, South Queensferry, UK). Samples were included for microarray analysis if the RNA integrity number (RIN) was > 7.
Label biotin
Label protocol One hundred nanogram of total RNA was used for whole transcript cDNA synthesis with the Whole-Transcript Sense Target Assay (Affymetrix, Santa Clara, CA, USA; P/N 900652).
 
Hybridization protocol Samples were hybridized to Affymetrix GeneChip Human Gene 1.1 ST array plates (Santa Clara, CA) according to manufacturer's instructions.
Scan protocol Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).
Data processing Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.36.1).
 
Submission date Jul 15, 2016
Last update date Apr 25, 2018
Contact name Guido Hooiveld
E-mail(s) guido.hooiveld@wur.nl
Organization name Wageningen University
Department Div. Human Nutrition & Health
Lab Nutrition, Metabolism & Genomics Group
Street address HELIX, Stippeneng 4
City Wageningen
ZIP/Postal code NL-6708WE
Country Netherlands
 
Platform ID GPL11532
Series (1)
GSE84453 Pure epicatechin and inflammatory gene expression profiles in circulating immune cells in (pre) hypertensive adults; a randomized double-blind, placebo-controlled, crossover trial

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

Data table
ID_REF VALUE
7892501 5.404858117
7892502 5.466784441
7892503 4.151559969
7892504 7.348214804
7892505 2.608028441
7892506 6.038870791
7892507 4.258315176
7892508 6.767914945
7892509 9.295813403
7892510 5.120041895
7892511 3.630605615
7892512 5.39139696
7892513 3.726007798
7892514 9.021215143
7892515 8.474254206
7892516 4.739426421
7892517 6.001080198
7892518 2.365365959
7892519 4.644081924
7892520 8.496465

Total number of rows: 33297

Table truncated, full table size 646 Kbytes.




Supplementary file Size Download File type/resource
GSM2236501_033_213JJT1_B_G166_A05.CEL.gz 4.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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