Vaccinium acuminatissimum - GEO DataSets

(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 darrowii; Vaccinium corymbosum

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

Platforms:: GPL33769 GPL33280
36 Samples

Download data: BW, CGMAP

Series

Accession:: GSE228041

ID:: 200228041

PubMed Full text in PMC Similar studies

Select item 2002370784.

MicroRNA profiling in Caco-2BBe1 cells in response to cranberry proanthocyanidin or its metabolites with and without IL-1β

(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

Series

Accession:: GSE237078

ID:: 200237078

PubMed Full text in PMC Similar studies Analyze with GEO2R

Select item 2002546335.

Prebiotic proanthocyanidins inhibit bile reflux-induced esophageal adenocarcinoma through reshaping the gut microbiome

(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

Series

Accession:: GSE254633

ID:: 200254633

PubMed Full text in PMC Similar studies

Select item 2002052406.

Transcriptional profiling of extraintestinal Escherichia coli exposed to cranberry pomace extracts alone or in combination with ceftriaxone

(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

Series

Accession:: GSE205240

ID:: 200205240

Select item 2001684467.

Analysis of Transcriptomics and Rhizosphere Fungal Diversity in Different Tissues of Blueberry under Cadmium Stress

(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

Series

Accession:: GSE168446

ID:: 200168446

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001605658.

Cranberry proanthocyanidins and dietary oligosaccharides synergistically modulate Lactobacillus plantarum physiology

(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

Series

Accession:: GSE160565

ID:: 200160565

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 2001195549.

Transcriptomic analysis of plant Cd-regulated genes in the ericoid mycorrhizal symbiosis

(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:: Vaccinium myrtillus; Oidiodendron maius Zn

Type:: Expression profiling by high throughput sequencing

Platforms:: GPL25516 GPL25535
12 Samples

Download data: FASTA, TXT

Series

Accession:: GSE119554

ID:: 200119554

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20011926610.

Transcriptomic analysis of fungal Cd-regulated genes in the ericoid mycorrhizal symbiosis

(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:: GPL25516 GPL25514
12 Samples

Download data: TXT

Series

Accession:: GSE119266

ID:: 200119266

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20013748311.

Impact of urine from cranberry-treated volunteers on global gene expression of uropathogenic Escherichia coli

(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

Series

Accession:: GSE137483

ID:: 200137483

SRA Run Selector

Select item 20012753012.

NCBI GEO Submission of human whole blood transcriptomes in response to a high-fat meal

(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

Series

Accession:: GSE127530

ID:: 200127530

Select item 20006616813.

Transcript profiling of Pinus sylvestris trees as a response to Heterobasidion annosum infection under field conditions

(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

Series

Accession:: GSE66168

ID:: 200066168

Analyze with GEO2R

Select item 20011609514.

Identification of Exosome-Like Nanoparticle Derived MicroRNAs from Eleven Edible Plants

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

Type:: Non-coding RNA profiling by high throughput sequencing

11 related Platforms
11 Samples

Download data: TXT, XLSX

Series

Accession:: GSE116095

ID:: 200116095

SRA Run Selector

Select item 20010784515.

Gene expression changes in Meliniomyces bicolor- Vaccinium myrtillus mycorrhizal roots compared to Meliniomyces bicolor free-living mycelium

(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

Series

Accession:: GSE107845

ID:: 200107845

SRA Run Selector

Select item 20010764716.

Gene expression changes in Rhizoscyphus ericae UMAH 7357- Vaccinium myrtillus mycorrhizal roots compared to Rhizoscyphus ericae UMAH 7357 free-living mycelium

(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

Series

Accession:: GSE107647

ID:: 200107647

SRA Run Selector

Select item 20009441117.

Identification of conserved and novel microRNAs in blueberry

(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

Series

Accession:: GSE94411

ID:: 200094411

PubMed Full text in PMC Similar studies SRA Run Selector

Select item 20006727718.

Liver tissue HELP-tagging cytosine methylation data from C57BL/6J mice receiving high-fat diet with or without lingonberries

(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

Series

Accession:: GSE67277

ID:: 200067277

PubMed Similar studies SRA Run Selector

Select item 20006671119.

Expression data from livers from mice receiving high-fat (HF) diets supplemented with different berries

(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

Series

Accession:: GSE66711

ID:: 200066711

Analyze with GEO2R

Select item 20006394720.

Transcriptome comparison of ectomycorrhizal, ericoid and orchid mycorrhizal fungi

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

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

Type:: Expression profiling by high throughput sequencing

10 related Platforms
42 Samples

Download data: TXT

Series

Accession:: GSE63947

ID:: 200063947

PubMed Full text in PMC Similar studies

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