Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Aquatic microbiome introduced via hydroponic system

PROVIDER: PRJNA1269763 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR33770500.fastq.gz	Fastqsanger.gz
	SRR33770501.fastq.gz	Fastqsanger.gz
	SRR33770494.fastq.gz	Fastqsanger.gz
	SRR33770495.fastq.gz	Fastqsanger.gz
	SRR33770496.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Project description:Hydroponic/ Aquaponic microbiome

| PRJNA785644 | ENA

rhizosphere metagenome

Project description:Hydroponic tomato rhizospheric microbiome

| PRJNA984704 | ENA

MiSSEel - MicroRNA Sequencing in Stressed Eels

Project description:This project aims to study the role played by small non-coding RNAs in the response of aquatic organisms to the presence of micropollutants in the environment. MiRNA were purified from Eels (Anguilla anguilla) sampled from two sites along the Gironde aquatic system with contrasted pollution profiles.

2019-04-09 | GSE109689 | GEO

Gene expression profile of Oryza longistaminata ramet pair roots in response to different nitrogen conditions

Project description:Oryza longistaminata, a wild rice, vegetatively reproduces and forms a networked clonal colony consisting of ramets connected by rhizomes. Although water, nutrients, and other molecules can be transferred between ramets via the rhizomes, inter-ramet communication in response to spatially heterogeneous nitrogen availability is not well understood. We analyzed the transcriptomic response of ramet pairs to heterogeneous nitrogen availability by using a split hydroponic system that allowed each ramet root to be exposed to different conditions.

2021-08-23 | GSE182486 | GEO

Gene expression profiles for genetically engineered human hepatoma HepG2/8F_HS cells with or without heat treatment, cultured as monolayer or spheroids

Project description:We developed genetically engineered HepG2/8F_HS cells, in which eight liver-enriched transcription factor (LETF) genes—hepatocyte nuclear factor (HNF)-1α, HNF-1β, HNF-3β, HNF-4α, HNF-6, CCAAT/enhancer binding protein (C/EBP)-α, C/EBP-β and C/EBP-γ— under the control of TRE/PCMVmin promoter were introduced into a previously developed human hepatoma cell line (HepG2-HSP). The heat-inducible synthetic promoter system was introduced into HepG2 cells and tetracycline-responsive transactivator (tTA) and enhanced green fluorescent protein (EGFP) were expressed via positive feedback of tTA transcription in response to heat treatment. HepG2/8F_HS cells can induce high liver functions by heat treatment via overexpression of LETF genes.

2022-04-04 | E-MTAB-11486 | biostudies-arrayexpress

EcoFAB 2.0 Root Microbiome Ring Trial

Project description:The experiment aimed to demonstrate the reproducibility of microbiome formation, metabolite production, and plant growth across multiple laboratories using the EcoFAB 2.0 system. To achieve this, five laboratories (A-E) conducted the identical experiment. In each laboratory, Brachypodium distachyon Bd21-3 was grown in the EcoFAB 2.0 system and subjected to the following treatments: an axenic (mock-inoculated) plant control, two synthetic communities SynCom16 or SynCom17 (+/-Burkholderia sp. OAS925, a strong root colonizer), or a plant-free medium control. Each treatment was replicated seven times (n=7). After 22 days, the spent hydroponic growth medium was collected and analyzed using polar HILIC metabolomics to determine the exometabolite composition.

2024-07-29 | MSV000095476 | MassIVE

Targeted DamID to understand transcription factor genomic occupancy in human foetal lung progenitor cells

Project description:In order to study the genomic occupancy of transcription factors, including SOX9, ETV4 and ETV5, in human foetal lung tip progenitor cells, we have introduced Targeted DamID system via lentivirus in a human foetal lung tissue derived organoid culture (Nikolic et al., 2017). We were able to identify the corresponding TF motif enrichment and discovered a potential co-regulation function of SOX9 and ETV factors in human feotal lung progenitor cells. This study has pioneered the use of targeted DamID approach in tissue derived organoid system.

2022-04-30 | GSE189786 | GEO

Effect of doxycycline on the gut microbiome and neuroinflammation

Project description:Abstract: Many mouse models of neurological disease use the tetracycline transactivator (tTA) system to control transgene expression by oral treatment with the broad-spectrum antibiotic doxycycline. Antibiotic treatment used for transgene control might have undesirable systemic effects, including the potential to affect immune responses in the brain via changes in the gut microbiome. Recent work has shown that an antibiotic cocktail to perturb the gut microbiome can suppress microglial reactivity to brain amyloidosis in transgenic mouse models of Alzheimer's disease based on controlled overexpression of the amyloid precursor protein (APP). Here we assessed the impact of chronic low dose doxycycline on gut microbiome diversity and neuroimmune response to systemic LPS challenge in a tTA-regulated model of Alzheimer's amyloidosis. We show that doxycycline decreased microbiome diversity in both APP transgenic and wild-type mice and that these changes persisted long after drug withdrawal. Despite this change in microbiome composition, dox treatment had minimal effect on transcriptional signatures in the brain, both at baseline and following acute LPS challenge. Our findings suggest that central neuroinflammatory responses may be less affected by dox at doses needed for transgene control than by antibiotic cocktail at doses used for microbiome manipulation.

2024-01-10 | GSE236242 | GEO

Transcriptional response of tea roots of different genotypes to potassium

Project description:Purpose: We investigated root foraging strategies for K of tea plants using a multi-layer split-root system by RNA-seq. Methods: One-year old tea cuttings were cultivated with the roots evenly planted on the two sides of the split root hydroponic box with a root canal. Three treatments were included to simulate the heterogeneous and homogeneous K environments. After 5d treatment, the roots on the two sides of the split root hydroponic box were collected separately and the RNA sequencing were analyzed by the Illumina Hiseq (2500, Illumina, San Diego, CA). Results: RNA-seq data had a linear relationship with qRT–PCR (r2=0.76), which confirmed the reliability of the RNA-seq data. Conclusions: Our study screened the key genes of tea root system to adapt to potassium heterogeneity.

2022-08-17 | GSE198198 | GEO

Changes in intestinal permeability and gut microbiota following diet-induced weight loss in patients with metabolic dysfunction-associated steatohepatitis and liver fibrosis

Project description:We explore whether a low-energy diet intervention for Metabolic dysfunction-associated steatohepatitis (MASH) improves liver disease by means of modulating the gut microbiome. 16 individuals were given a low-energy diet (880 kcal, consisting of bars, soups, and shakes) for 12 weeks, followed by a stepped re-introduction to whole for an additional 12 weeks. Stool samples were obtained at 0, 12, and 24 weeks for microbiome analysis. Fecal microbiome were measured using 16S rRNA gene sequencing. Positive control (Zymo DNA standard D6305) and negative control (PBS extraction) were included in the sequencing. We found that low-energy diet improved MASH disease without lasting alterations to the gut microbiome.

2024-12-31 | E-MTAB-14061 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data