GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Vaccinium corymbosum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing

Platform:

GPL33280

15 Samples

Download data: BW

(Submitter supplied) Characterization of WGBS and RNA-seq in blueberry fruits

Organism:

Vaccinium corymbosum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33280

15 Samples

Download data: BW

(Submitter supplied) We did whole-genome methylation sequencing for 21 Vaccinium samples. This project attempts to analyze the improvement breeding process of cultivated blueberry from two aspects of heredity and epigenetic inheritance.

Organism:

Vaccinium corymbosum; Vaccinium darrowii

Type:

Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL33280 GPL33769

36 Samples

Download data: BW, CGMAP

(Submitter supplied) The molecular basis underlying the known anti-inflammatory and anticarcinogenic properties of cranberries is incompletely understood. We investigated the microRNA (miRNA)-modulatory effects of cranberry proanthocyanidin (PAC) and two of its main gut microbial metabolites, 3,4-dihydroxyphenylacetic acid (DHPAA) and 3-(4-hydroxyphenyl)-propionic acid (HPPA), in intestinal cells at homeostasis and in inflammatory conditions. more...

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL24158

36 Samples

Download data: TXT

(Submitter supplied) The gut and local esophageal microbiome progressively shift from healthy commensal bacteria to inflammatory-linked pathogenic bacteria in patients with gastroesophageal reflux disease, Barrett’s esophagus and esophageal adenocarcinoma (EAC). However, mechanisms by which microbial communities contribute to reflux-driven EAC remain incompletely understood and challenging to target. Herein, we utilized a rat reflux-induced EAC model to investigate targeting the gut microbiome-esophageal metabolome axis with cranberry proanthocyanidins (C-PAC) to inhibit EAC progression. more...

Organism:

rat gut metagenome

Type:

Other

Platform:

GPL24042

25 Samples

Download data: CSV

(Submitter supplied) To investigate the effects of ceftriaxone and cranberry pomace extract on transcriptome of extraintestinal E. coli (ExPEC)

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28126

12 Samples

Download data: TSV

(Submitter supplied) In this study, blueberry transcriptomics and rhizosphere fungal diversity were analyzed by simulated potting method to treat blueberries with Cd stress, and the content of Fe, Mn, Cu, Zn and Cd in each tissue, soil and DGT of blueberries were determined. , Combined with transcriptomics for correlation analysis. A total of 84374 annotated genes were obtained in blueberry roots, stems, leaves and fruits, of which 3370 DEGs were found, and DEGs in the stem accounted for the highest proportion, totaling 2521. more...

Organism:

Vaccinium ashei

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29820

24 Samples

Download data: FASTA, TXT

(Submitter supplied) Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their gut microbiome. Based on previous observations, we hypothesized thatprobiotic Lactobacillus plantarum interact with cranberry polyphenols and dietary oligosaccharides to synergistically impact its physiology. In this study, L. plantarum ATCC BAA-793 was grown on dietary oligosaccharides including cranberry xyloglucans, fructooligosaccharides, and human milk oligosaccharidesin conjunction with proanthocyanidins (PACs) extracted from cranberry. more...

Organism:

Lactiplantibacillus plantarum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29328

22 Samples

Download data: CSV, TXT

(Submitter supplied) Illumina HiSeq2000 technology was used to generate mRNA profiles from Vaccinium myrtillus mycorrhizal and non-mycorrhizal roots with or without Cadmium treatment. 150bp reads were generated and aligned to a Vaccinium myrtillus de novo assembly as reference using CLC Genomics Workbench 8.

Organism:

Oidiodendron maius Zn; Vaccinium myrtillus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25516 GPL25535

12 Samples

Download data: FASTA, TXT

(Submitter supplied) Illumina HiSeq2000 technology was used to generate mRNA profiles from Oidiodendron maius free-living mycelium and Vaccinium myrtillus mycorrhizal roots with or without Cadmium treatment. 150bp reads were generated and aligned to the O.maius reference transcripts using CLC Genomics Workbench 8

Organism:

Vaccinium myrtillus; Oidiodendron maius Zn

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25514 GPL25516

12 Samples

Download data: TXT

(Submitter supplied) Growth in urine of cranberry extract-treated volunteers did not markedly affect the transcirptome of UPEC strain UTI89. Expression of bacterial adhesin determinants (P fimbriae, S fimbrae, curli) was not markedly changed upon growth in the urine samples, while a slight, but non-significant upregulation of type 1 fimbriae was observed.

Organism:

Escherichia coli

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21222

2 Samples

Download data: XLSX

(Submitter supplied) Modern humans spend most of their time having eaten recently. The purpose of the current project is to understand how the blood, which contains immune cells, responds in the hours after eating a meal that is moderately high in fat. We used a sequencing method to observe the expression of all the genes in blood cells in five participants who were each fed a high fat meal on three separate days. The results are reported in the manuscript, “Temporal changes in postprandial blood transcriptomes reveal subject-specific pattern of expression of innate immunity genes after a high-fat meal."

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

45 Samples

Download data: TXT

(Submitter supplied) In conifer forests of Northern Europe, a pathogenic fungus Heterobasidion annosum attacks the roots of Scots pine and causes mortality. Trees with infection grow slower and produce less timber with reduced quality. Despite applied control methods, such as switching tree species to a non-host species, or stump treatment, root and butt rot continues to be a serious forest health problem. Disease resistance breeding is a less-applied control method which has potential to improve tree health. more...

Organism:

Pinus sylvestris

Type:

Expression profiling by array

Platform:

GPL19078

24 Samples

Download data: PAIR

(Submitter supplied) In this study, we found that the highly expressed miRNAs appear in EPDELNs (Edible plant-derived exosome-like nanoparticles) have the potential to regulate human mRNA in a cross-kingdom manner. Target prediction and functional analysis revealed that highly expressed miRNAs were closely associated with inflammatory responses and cancer-related pathways. Therefore, we hypothesized that miRNAs in EPDELNs may be a crucial factor behind the regulatory function of EPDELNs.

Organism:

Solanum lycopersicum; Actinidia chinensis; Cucumis melo; Pisum sativum; Vaccinium; Cocos nucifera; Citrus x paradisi; Pyrus; Citrus reticulata; Glycine max; Zingiber officinale

Type:

Non-coding RNA profiling by high throughput sequencing

11 related Platforms

11 Samples

Download data: TXT, XLSX

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles from Meliniomyces bicolor mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 113 days and used for RNA extraction. Reads of 150bp were generated and aligned to Meliniomyces bicolor transcripts (https://genome.jgi.doe.gov/Melbi2/Melbi2.home.html) using CLC Genomics Workbench 8.

Organism:

Hyaloscypha bicolor

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24356

6 Samples

Download data: TXT

(Submitter supplied) Illumina HiSeq technology was used to generate mRNA profiles fromRhizoscyphus ericae UMAH 7357 mycorrhizal roots compared to free-living mycelium . Mycorrhizal roots and control mycelium were harvested after 75 days and used for RNA extraction. Reads of 150bp were generated and aligned to Rhizoscyphus ericae UMAH 7357 transcripts (https://genome.jgi.doe.gov/Rhier1/Rhier1.home.html) using CLC Genomics Workbench 8.

Organism:

Hyaloscypha hepaticicola

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24332

6 Samples

Download data: TXT

(Submitter supplied) In the present study, we employed the high-throughput sequencing technology to profile miRNAs in blueberry fruits. A total of 9,992,446 small RNA tags with sizes ranged from 18 to 30 nt were obtained, indicating that blueberry fruits have a large and diverse small RNA population. Bioinformatic analysis has identified 412 conserved miRNAs, which belong to 20 families, and 57 predicted novel miRNAs likely unique to blueberries. more...

Organism:

Vaccinium ashei

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL23634

1 Sample

Download data: FA

(Submitter supplied) The C57BL/6J mouse model develops obesity and pre-diabetes when fed a high-fat diet. In this experiment, DNA methylation was assessed globally at specific CpG sites in liver tissue from mice receiving high-fat diet (45E% from fat) for 13 weeks (Control) or high-fat diet supplemented with 20% (w/w) of freeze-dried lingonberries (n=4). Our findings show that lingonberries prevent development of high-fat induced obesity, hepatic steatosis and low-grade inflammation, and the DNA was hypermethylated in mice receiving lingonberries compared to control.

Organism:

Mus musculus

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: TXT

(Submitter supplied) DNA microarray analysis was employed to analyze hepatic gene expression in mice that were protected against HF-induced obesity and liver steatosis (ie HF diets supplemented with lingonberries, blackcurrants or bilberries) and compare to mice who were not protected (HF control) or even experienced increased obesity and fatty liver (HF diet with açai). The study was done to increase understanding of underlying mechanisms of the observed effects.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6887

36 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Paxillus involutus; Piloderma croceum; Serendipita vermifera; Suillus luteus; Amanita muscaria; Hebeloma cylindrosporum; Oidiodendron maius; Tulasnella calospora

Type:

Expression profiling by high throughput sequencing

10 related Platforms

42 Samples

Download data: TXT