Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sweetpotato microbiome at two North Carolina farms

ABSTRACT: Surveying the sweetpotato rhizosphere, endophyte, and surrounding soil microbiomes at two North Carolina farms reveals underpinnings of sweetpotato microbiome community assembly

PROVIDER: PRJEB29367 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2856530_1.fastq.gz	Fastqsanger.gz
	ERR2856530_2.fastq.gz	Fastqsanger.gz
	ERR2856540_1.fastq.gz	Fastqsanger.gz
	ERR2856540_2.fastq.gz	Fastqsanger.gz
	ERR2856550_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 430

Similar Datasets

High throughput sequencing identifies chilling responsive genes in sweetpotato (Ipomoea batatas Lam.) during storage

Project description:Sweetpotato (Ipomoea batatas L.) is a globally important economic food crop. It belongs to Convolvulaceae family and origins in the tropics; however, sweetpotato is sensitive to cold stress during storage. In this study, we performed transcriptome sequencing to investigate the sweetpotato response to chilling stress during storage. A total of 110,110 unigenes were generated via high-throughput sequencing. Differentially expressed genes (DEGs) analysis showed that 18,681 genes were up-regulated and 21,983 genes were down-regulated in low temperature condition. Many DEGs were related to the cell membrane system, antioxidant enzymes, carbohydrate metabolism, and hormone metabolism, which are potentially associated with sweetpotato resistance to low temperature. The existence of DEGs suggests a molecular basis for the biochemical and physiological consequences of sweetpotato in low temperature storage conditions. Our analysis will provide a new target for enhancement of sweetpotato cold stress tolerance in postharvest storage through genetic manipulation.

2024-02-06 | GSE255226 | GEO

Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

Project description:Investigation of whole transcriptome gene expression level during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87 Identification of transcription factors (TFs) during tuberous root formation and development in sweetpotato (Ipomoea batatas) cv. Guangshu 87 A total of 7 samples were analyzed using RNA isolated from sweetpotato roots at 10, 15, 20, 30, 60, 90, 120days after transplanting. Each sample had two biological replicates.

2015-07-12 | E-GEOD-48834 | biostudies-arrayexpress

Temporal patterns of gene expression associated with tuberous root formation and development in sweetpotato (Ipomoea batatas)

2015-07-12 | GSE48834 | GEO

A reanalysis: Do hog farms cause disease in North Carolina neighborhoods?

Project description:A 2018 publication reported that communities living near hog Concentrated Animal Feeding Operations (CAFO) in North Carolina, USA have increased negative health outcomes and mortalities. While the authors stated that the associations do not imply causation, speculative interpretation of their results by media and subsequent use as evidence in lawsuits caused detrimental effects on the swine industry. We repeated their study using updated data to evaluate the strength of conclusions and appropriateness of methods used with the ultimate goal of alerting on the impact that study limitations may have when used as evidence. As done in the 2018 study, logistic regression was conducted at the individual level using 2007-2018 data, while presumably correcting for six confounders drawn from zip code or county-level databases. Exposure to CAFOs was defined by categorizing zip codes into three by swine density; where, >1 hogs/km2 (G1), > 232 hogs/km2 (G2), and no hogs (Control). Association with CAFO exposure resulting in mortality, hospital admissions, and emergency department visits were analyzed related to eight conditions (six from the previous study: anemia, kidney disease, infectious diseases, tuberculosis, low birth weight, and we added HIV and diabetes). Re-evaluation identified shortcomings including ecological fallacy, residual confounding, inconsistency of associations, and overestimation of exposure. HIV and diabetes, which are not causally relatable to CAFOs, were also prominent in these neighborhoods likely reflecting underlying systemic health disparities. Hence, we emphasize the need for improved exposure analysis and the importance of responsible interpretation of ecological studies that affect both public health and agriculture.

| S-EPMC9945130 | biostudies-literature

Assessing the remarkable morphological diversity and transcriptomic basis of leaf shape in Ipomoea batatas (sweetpotato)

Project description:Leaf shape is a spectacularly diverse trait that influences various aspects of plant physiology, and is even correlated with crop yield and quality in multiple species. However, only a few genetic dissections of leaf shape have been accomplished at a species-wide level. Here, we perform an initial characterization of leaf shape variation in Ipomoea batatas, the sweetpotato, at multiple scales of analysis. We use a transcriptomic survey to identify gene expression changes associated with two commonly studied leaf shape traits--circularity and aspect ratio using 19 individuals (accession) of sweetpotato. We comprehensively describe the remarkable morphological diversity in leaf shape in sweetpotato, and identify 147 differentially regulated genes associated with circularity and aspect ratio, providing an initial set of hypotheses regarding the genetic basis of leaf shape in this species.

2019-08-31 | GSE128065 | GEO

Swine farms

Project description:Swine farms Raw sequence reads

| PRJNA1155291 | ENA

ALUS farms

Project description:Arthropod monitoring at ALUS Farms 2019

| PRJNA856887 | ENA

Genome-wide analysis of tumor-infiltrating dendritic cells comparing C57BL/6 mice obtained from Jackson laboratories or Taconic farms, untreated or treated with Bifidobacterium.

Project description:Comparison of gene expression in dendritic cells (DCs) isolated from tumors of C57BL/6 obtained from Taconic farms vs DCs isolated from tumor of C57BL/6 mice obtained from Jackson Labortaory vs DCs isolated from tumors of C57BL/6 obtained from Taconic farms and orally gavaged with Bifidobacterium prior to tumor implantation

2015-11-12 | GSE73475 | GEO

A feasibility study of conducting surveillance for swine pathogens in slurry from North Carolina swine farms.

Project description:Despite close contact between humans and animals on large scale farms, little to no infectious disease research is conducted at this interface. Our goal in this preliminary study was to explore if we could detect swine pathogens using a non-invasive, indirect approach through the study of swine slurry. From April to November 2018, 105 swine slurry samples were collected by farm personnel from waste pits at two sites on a swine farm in North Carolina. These samples were tested for DNA and RNA viruses using a real-time PCR and RT-PCR. Statistical analyses were performed to measure association between virus positive outcomes and potential predictors such as date of sample collection, weight of pigs, number of pigs in barn, temperature, and weather conditions. Overall, 86% of the samples had evidence of at least one of the targeted viruses. Ultimately, this study demonstrated the utility of conducting noninvasive surveillance for swine pathogens through the study of swine slurry. Such swine slurry surveillance may supplant the need to handle, restrain, and collect specimens directly from pigs thus providing an approach to emerging pathogen detection that appeals to the swine industry.

| S-EPMC7308328 | biostudies-literature

FARMS-SAFE

Project description:Bacterial genome sequences of isolates from farms in Argentina

| PRJEB70722 | ENA