Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Metagenomic of caves, Brazil

PROVIDER: PRJNA896164 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR22133539_1.fastq.gz	Fastqsanger.gz
	SRR22133539_2.fastq.gz	Fastqsanger.gz
	SRR22133540_1.fastq.gz	Fastqsanger.gz
	SRR22133540_2.fastq.gz	Fastqsanger.gz
	SRR22133541_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 60

Similar Datasets

Project description:Caves Metagenomic

| PRJNA695576 | ENA

Project description:Metagenomic from two Pakistan's caves

| PRJNA741999 | ENA

Zika virus strain:Brazil ZKV

Project description:Brazil ZKV Metagenomic assembly

| PRJNA306240 | ENA

Environmental metagenome from CAVES

Project description:CAVES Metagenome

| PRJNA610730 | ENA

Bats

Project description:Viral Metagenomic of neotropical bats from Brazil

| PRJNA557656 | ENA

Cave bacterial diversity

Project description:Metagenomic study of bacterial diversity in Caves of Mizoram, Northeast India

| PRJEB7730 | ENA

Project description:Metagenomic Analysis of Bat Gut and Guano Microbiome from Caves in CALABARZON

| PRJNA1096155 | ENA

Project description:Viral metagenomics analysis of Antricola ticks collected in bat caves in the western Amazonia of Brazil

| PRJNA577110 | ENA

Comparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis

Project description:The Global Pandemic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genome of three Bd-GPL strains have enabled studies of the pathogen but the genomic features that set Bd-GPL apart from other Bd lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used long-read DNA sequencing to assemble high-quality genomes of three Bd-BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii (Ps) strain JEL0888, and compared these to genomes of previously sequenced Bd-GPL strains. The Bd-BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. Our pan-genome analysis provided insight into shared and lineage-specific gene content. The core genome of Bd consists of 6278 conserved gene families, with 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered gene copy number variation in pathogenicity gene families between Bd-BRAZIL and Bd-GPL strains though none were consistently expanded in Bd-GPL or Bd-BRAZIL strains. Comparison within the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified variation in sequence and protein domain counts. We further test these new Bd-BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these genomes as reference genomes for future studies.

2024-01-31 | GSE253912 | GEO

Molecular classifiers for follicular adenomas

Project description:Patients were recruited at the Hospital do Cancer AC Camargo (SÃ£o Paulo/Brazil), Instituto de Enfermedades Neoplasicas - INEN (Lima, Peru), Hospital Araujo Jorge (Goiania, Brazil) and Hospital Heliopolis (SÃ£o Paulo, Brazil).All patients signed a pre-informed consent and the study was approved by the internal ethics committee. Tissue samples were snap frozen in liquid nitrogen . Before RNA extraction histopathological diagnosis was re-confirmed, all samples were micro-dissected and only tissues with at least 70% of tumor cells and no visible infiltrating inflammatory cells were used as tumor. Morphologically disease-free tissue obtained from surgical margins was considered as normal. A total of 38 samples were analyzed: 8 normal tissues, 10 goiters, 10 adenomas and 10 papillary carcinomas. Keywords: other

2010-06-10 | E-GEOD-2468 | 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