Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ISO_soil_bacteria_fungi_diversity_study

ABSTRACT: Meta-barcoded evaluation of the ISO Standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

PROVIDER: PRJEB4825 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR359761.fastq.gz	Fastqsanger.gz
	ERR359762.fastq.gz	Fastqsanger.gz
	ERR359763.fastq.gz	Fastqsanger.gz
	ERR359764.fastq.gz	Fastqsanger.gz
	ERR359765.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 89

Similar Datasets

Proteomic analysis of residues from experimental ceramics used for cooking a mixture of milk, meat and cereals

Project description:Ceramic vessels were used to cook a mixture of milk, meat (pork and beef) and cereals (wheat and barley), and proteomic studies were conducted on the ceramics to study the absorption and subsequent extraction and identification of the proteins from th various categories of foodstuff. A novel Deep Eutectic Solvent-based extraction procedure was also trialled and its efficacy compared with the standard GuHCl-based extraction procedure.

2022-11-11 | PXD028994 | Pride

Improved genome annotation of the fungal wheat pathogen Zymoseptoria tritici IPO323 using Iso-Seq and RNA-Seq data

Project description:To reannotate the genome of Zymoseptoria tritici IPO323, RNA-Seq and Iso-Seq runs were performed on different growth media to provide new source of evidence for gene model predictors. New gene models were predicted and combined with existing annotation releases. Finally, selection of best gene models was done by congruence with evidence data like transcript assembled from RNA-Seq, Iso-Seq cDNA and fungal proteins from databases.

2023-07-04 | GSE218898 | GEO

Comparative transcriptomic characterisation of canine prostate fine-needle-aspiration and tissue samples - from sampling to sequencing

Project description:Ultrasound-guided fine-needle aspiration (US-FNA) biopsy is a widely used minimally invasive sampling procedure for cytological diagnosis. This study investigates the feasibility of using US-FNA samples for both cytological diagnosis and whole transcriptome RNA-sequencing analysis (RNA-Seq), with the ultimate aim of improving canine prostate cancer management. The feasibility of the US-FNA procedure was evaluated intra vitam on 43 dogs. Additionally, aspirates from 31 euthanised dogs were collected for standardising the procedure. Each aspirate was separated into two subsamples: for cytology and RNA extraction. Additional prostate tissue samples served as control for RNA quantity and quality evaluation, and differential expression analysis. The US-FNA sampling procedure was feasible in 95% of dogs. RNA isolation of US-FNA samples was successfully performed using phenol-chloroform extraction. The extracted RNA of 56% of a subset of US-FNA samples met the quality requirements for RNA-seq. Expression analysis revealed that only 153 genes were exclusively differentially expressed between non-malignant US-FNAs and tissues. Moreover, only 36 differentially expressed genes were associated with the US-FNA sampling technique and unrelated to the diagnosis. Furthermore, the gene expression profiles clearly distinguished between non-malignant and malignant samples. This proves US-FNA to be useful for molecular profiling.

2019-10-08 | GSE122916 | GEO

An optimized method for high-quality RNA extraction from distinctive intrinsic laryngeal muscles in the rat model

Project description:Challenges related to high-quality RNA extraction from post-mortem tissue have limited RNA-sequencing (RNA-seq) application in certain skeletal muscle groups, including the intrinsic laryngeal muscles (ILMs). The present study identified critical factors contributing to substandard RNA extraction from the ILMs and established a suitable method that permitted high-throughput analysis. Here, standard techniques for tissue processing were adapted, and an effective means to control confounding effects during specimen preparation was determined. The experimental procedure consistently provided sufficient intact total RNA (N = 68) and RIN ranging between 7.0 and 8.6, which was unprecedented using standard RNA purification protocols. This study confirmed the reproducibility of the workflow through repeated trials at different postnatal time points and across the distinctive ILMs. High-throughput diagnostics from 90 RNA samples indicated no sequencing alignment scores below 70%, validating the extraction strategy. Significant differences between the standard and experimental conditions suggest circumvented challenges and broad applicability to other skeletal muscles. This investigation remains ongoing given the prospect of therapeutic insights to voice, swallowing, and airway disorders. The present methodology supports pioneering global transcriptome investigations in the larynx previously unfounded in literature.

2022-11-06 | GSE217027 | GEO

Transcriptome analysis reveals anti-cancer effects of Isorhapontigenin (ISO) on human high invasive bladder cancer cells

Project description:Bladder cancer, the most common malignancy of the urinary tract, has a poor overall survival rate if the tumor becomes muscle invasive. The discovery and evaluation of new alternative medications targeting high-grade muscle invasive bladder cancer (MIBC) are of tremendous importance in reducing bladder cancer mortality. Isorhapontigenin (ISO), a stilbene derivative from Chinese herb Gnetum cleistostachyum, exhibits a strong anti-cancer effect on MIBCs. Here, we report the whole transcriptome profiling of ISO-treated human bladder cancer T24 cells. A total of 1047 differentially expressed genes (DEGs) were identified, including 596 downregulated and 451 upregulated genes. Functional annotation and pathway analysis revealed that ISO treatment induced massive changes in gene expression associated with cell movement, migration, invasion, metabolism, proliferation, and angiogenesis. Additionally, ISO treatment activated genes involved in the inflammatory response but repressed genes involved in hypoxia signaling, glycolysis, the actin cytoskeleton, and the tumor microenvironment. In summary, our whole transcriptome analysis demonstrated a shifted metabolism and altered actin cytoskeleton in ISO treated T24 cells, which subsequently contribute to tumor microenvironment remodeling that suppresses tumor growth and progression.

2024-02-14 | GSE252406 | GEO

Effect of 10 Cigarette Smoke Condensates on Primary Human Airway Epithelial Cells

Project description:Nine cigarette smoke condensates (CSCs) were produced under a standard ISO smoking machine regimen and one was produced by a more intense smoking machine regimen. These CSCs were used to treat primary normal human bronchial epithelial cells for 18 hours.

2009-09-24 | GSE18235 | GEO

AQS

Project description:Pyrosequencing of Bacterial rrs as Influenced by Soil DNA Extraction Procedure

| PRJEB2582 | ENA

Human skeletal muscle

Project description:Standard Affymetrix procedure, RNA from frozen tissue Keywords: equivalent probe

2003-12-10 | GSE595 | GEO

Cardiac fibroblasts behave differently to isoproterenol-induced injury based on their genetic variability

Project description:The goal of this study is to characterize molecular mechanisms that regulate cardiac fibrosis This study compare the fibrotic response of ISO-treated hearts in 3 strains of mice (B6, C3H and KK)

2018-07-02 | GSE109376 | GEO

Reconstruction evolutionary history of S. cerevisiae x S. kudriavzevii hybrids from wine beer dietetic supplement and clinical isolate

Project description:The aim of this experiment is to characterize the genome composition of the two hybrids IF6 and MR25. IF6 and MR25 are hybrids among S.cerevisiae and S. kudriavzevii. The hybridization of the genome extraction with the microarray was at 65C, under this condition only S. cerevisiae genes can hybridize. In this case we are only studying the genome composition of S. cerevisiae parental in the hybrids. The study of S. kudriavzevii parental genome was done by other methods.

2012-11-05 | E-MEXP-3375 | 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