{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":[null],"organism":["Homo sapiens"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-14563"],"description":["This study investigates the effects of fruit and vegetable (F&V) intake on biomarkers of chronic diseases in healthy human volunteers. The study uses a randomized crossover design with a total duration of 7 weeks. Each participant underwent a 2-week run-in period to standardize F&V intake at 50g per day, followed by two separate 2-week intervention phases, during which F&V intake was increased to 450g per day, with a 1-week washout period between interventions. Participants were randomized to receive two out of seven different nutrition interventions, each providing distinct combinations of F&V.  Blood samples were collected at baseline and after each intervention phase. Whole blood was drawn into EDTA-coated tubes, and RNA was extracted using the Directzol RNA microprep kit (ZY-R2052, Zymo Research), following ribo-depletion of rRNA. RNA quality and concentration were checked using a Qubit Fluorometer and Bioanalyzer. Samples with RIN values greater than 7 were used for library preparation.  Library preparation was performed using the NextFlex Rapid Directional RNA kit 2.0 with ribo-depletion, followed by sequencing on the Illumina platform (200-cycle S4 flow cells). Sequencing generated paired-end reads of 150bp from approximately 150 samples per flow cell. The resulting fastq files were processed, de-multiplexed, and reviewed for quality, and all samples from each participant were analyzed in batches. Data analysis focused on differential gene expression related to antioxidant capacity, inflammation, and DNA damage markers."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - RNA libraries were prepared using the NextFlex Rapid Directional RNA kit 2.0 with ribo-depletion (Perkin Elmer, Waltham, MA, USA). Approximately 100 ng of total RNA was used for each library preparation, with ribo-depletion carried out to remove rRNA. The libraries were constructed following the manufacturer's guidelines and were normalized according to RNA concentration and library size. The prepared libraries were checked for quality and fragment size distribution using a Bioanalyzer (Agilent Technologies).","Sample Collection - Whole blood samples were collected from participants using standard venipuncture techniques into EDTA-coated tubes during specific test days. On the collection day, participants arrived at the research facility after fasting overnight. Immediately after blood collection, the samples were transferred into freezer-safe Eppendorf tubes containing RNAlater solution (Ambion, Austin, TX, USA) in a 2:1 ratio (RNAlater to blood volume). This step was taken to stabilize the RNA in the samples. The tubes were then stored at -80°C until further processing. The samples were collected both at baseline and post-intervention phases, ensuring uniform handling across all time points.","Sequencing - Sequencing was performed on an Illumina platform (San Diego, CA, USA) using three 200-cycle S4 flow cells. Paired-end sequencing (150 bp read length) was carried out across approximately 150 samples per flow cell. The sequencing run generated fastq files, which were de-multiplexed, quality-checked, and reviewed for downstream analysis.","Nucleic Acid Extraction - RNA extraction from the blood samples was performed using the Directzol RNA microprep kit (ZY-R2052, Zymo Research), following the manufacturer's protocol. Before extraction, the blood samples were thawed on ice, and the RNAlater solution was removed by centrifugation at 5000× g for 1 minute. After the supernatant was discarded, 1xPBS (phosphate-buffered saline) was added to wash the pellet, followed by centrifugation to remove remaining impurities. QIAzol lysis reagent (QIAGEN) was then added at a 3:1 ratio, and the mixture was vortexed to ensure thorough lysis. Chloroform was added for phase separation, and the samples were centrifuged at 1200× g for 15 minutes at 4°C. The RNA-containing aqueous phase was transferred to a new tube, mixed with ethanol, and processed using Directzol spin columns. The extracted RNA was eluted in RNase-free water, and RNA quality and concentration were measured using a Qubit Fluorometer (Life Technologies) and a Bioanalyzer (Agilent Technologies). Only samples with RIN (RNA Integrity Number) greater than 7 were used for further analysis."],"figure_sub":["MINSEQE Score","Assays and Data","organisation","MAGE-TAB Files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"pubmed_abstract":["Adequate fruit and vegetable (F and V) intake, as recommended by the World Health Organization (over 400 g/day), is linked to reduced chronic disease risk. However, human intervention trials, especially with whole F and V and in complex combinations, are lacking. The MiBlend Study explored the effects of various phytochemical-rich F and V combinations on chronic disease risk markers, phytochemical absorption, and gene expression in blood. This randomized cross-over study involved participants consuming two of seven different F and V blends for 2 weeks (450 g/day), following a 2-week low F and V intake period (50 g/day). Each blend represented major phytochemical classes (flavonoids, anthocyanins, carotenoids, and glucosinolates) or combinations thereof. Markers of chronic disease risk, including DNA damage, oxidative stress, and retinal microvasculature, were measured. Increasing F and V intake significantly improved plasma antioxidant capacity, DNA damage protection, and retinal arteriolar dilation. Flavonoid-rich, carotenoid-rich, and complex blends notably reduced DNA damage susceptibility. Anthocyanin-rich and carotenoid-rich interventions were most effective in boosting antioxidant capacity, while blends high in flavonoids, especially combined with anthocyanins, significantly improved retinal microvasculature. Gene expression analysis revealed changes in DNA repair, signal transduction, and transcription processes, indicating mechanisms for these health benefits. The study suggests specific F and V blends can provide targeted health improvements, emphasizing the importance of both overall F and V intake and the specific phytochemical composition for personalized preventive strategies."],"study_type":["RNA-seq of coding RNA"],"species":["Homo sapiens"],"pubmed_title":["Effects of Different Combinations of Phytochemical-Rich Fruits and Vegetables on Chronic Disease Risk Markers and Gene Expression Changes: Insights from the MiBLEND Study, a Randomized Trial.","Unveiling Cell-Type-Specific Immune Reactions in Human Blood Following Varied Fruit and Vegetable Blends Interventions"],"additional_accession":["ERP165523"],"pubmed_authors":["Yueqin He","DeBenedictis JN, Murrell C, Hauser D, van Herwijnen M, Elen B, de Kok TM, van Breda SG.","Yueqin He, Julia N. DeBenedictis, Simone G. van Breda and Theo M. de Kok"]},"is_claimable":false,"name":"RNA-seq of human blood samples from MiBLEND study on the effect of fruit and vegetable blends on gene expression","description":"This study investigates the effects of fruit and vegetable (F&V) intake on biomarkers of chronic diseases in healthy human volunteers. The study uses a randomized crossover design with a total duration of 7 weeks. Each participant underwent a 2-week run-in period to standardize F&V intake at 50g per day, followed by two separate 2-week intervention phases, during which F&V intake was increased to 450g per day, with a 1-week washout period between interventions. Participants were randomized to receive two out of seven different nutrition interventions, each providing distinct combinations of F&V.  Blood samples were collected at baseline and after each intervention phase. Whole blood was drawn into EDTA-coated tubes, and RNA was extracted using the Directzol RNA microprep kit (ZY-R2052, Zymo Research), following ribo-depletion of rRNA. RNA quality and concentration were checked using a Qubit Fluorometer and Bioanalyzer. Samples with RIN values greater than 7 were used for library preparation.  Library preparation was performed using the NextFlex Rapid Directional RNA kit 2.0 with ribo-depletion, followed by sequencing on the Illumina platform (200-cycle S4 flow cells). Sequencing generated paired-end reads of 150bp from approximately 150 samples per flow cell. The resulting fastq files were processed, de-multiplexed, and reviewed for quality, and all samples from each participant were analyzed in batches. Data analysis focused on differential gene expression related to antioxidant capacity, inflammation, and DNA damage markers.","dates":{"release":"2025-09-02T00:00:00Z","modification":"2025-09-02T01:02:31.286Z","creation":"2024-10-28T11:29:10.163Z"},"accession":"E-MTAB-14563","cross_references":{"ENA":["ERP165523"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003738","EFO_0004184"],"doi":["10.3390/antiox13080915"]}}