Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Bacteria

ABSTRACT: Bacterial NGS for comparative determination of AST

PROVIDER: PRJNA726883 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	JAGYQP01.dat.gz	Other
	JAGYQP01.fasta.gz	Fasta.gz
	JAGYQP01.master.dat	Other
	JAGYQQ01.dat.gz	Other

Items per page:

1 - 5 of 193

Similar Datasets

Bacteria

Project description:A project of associating bacterial WGS and AST data

| PRJDB7087 | ENA

Next Generation Sequencing facilitates to identify the differential expression genes of liver tissue from with liver injury(AST>40) or without liver injury(AST<40) from HBV-infected patients.

Project description:We obtained HBV-infected liver tissues from liver surgery(AST<40) and liver transplantation(AST>40) to perform next-generation sequencing (NGS). Illumina mRNA-seq sample preparation kit was used to perform paired-end library sequencing with Illumina HiSeq 2000 and sequence analysis was determined using the Illumina data analysis pipeline. Based on the comparison results, we performed the GO and KEGG pathway enrichment analysis. That might suggest the different status of HBV-infected liver from liver surgery(AST<40) and liver transplantation(AST>40).

2023-04-05 | GSE208637 | GEO

Bacteria

Project description:NGS

| PRJNA1057910 | ENA

Associated bacteria affect sexual reproduction by altering gene expression and metabolic processes in a biofilm inhabiting diatom (Seminavis robusta)

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of Seminavis robusta in presence and absence of associated bacterial spent medium (Maribacter sp. and Roseovarius sp.) in order to highlight the effect of bacterial exudates on diatom gene expression and metabolic processes.

2019-07-15 | GSE131727 | GEO

mRNA transcript distribution bias between Borrelia burgdorferi bacteria and their outer membrane vesicles

Project description:We performed comparative transcriptomic analysis of the outer membrane vesicles (OMVs) released from B. burgdorferi. We identified a total of ~1200 unique transcripts with at least one mapped read from the bacterial cell and its OMVs.

2018-06-21 | GSE114368 | GEO

Bacteria

Project description:CRISPR-Cas13b NGS data

| PRJNA358111 | ENA

Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours

Project description:In this study, we performed a comparative analysis of gut microbiota composition and gut microbiome-derived bacterial extracellular vesicles (bEVs) isolated from patients with solid tumours and healthy controls. After isolating bEVs from the faeces of solid tumour patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of faeces from patientsand controls using 16S rRNA sequencing. Machine learning was used to classify the samples into patients and controls based on their bEVs and faecal microbiomes.

2024-08-08 | PXD047510 | Pride

Human immunodeficiency virus 1

Project description:HIV-1 tropism determination Using NGS

| PRJDB3249 | ENA

Highly multiplexed spatial transcriptomics in bacteria

Project description:Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based, transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hindered by the massive density of bacterial mRNA. To overcome this challenge, we combine 1000-fold volumetric expansion with multiplexed error robust fluorescence in situ hybridization (MERFISH) to create bacterial-MERFISH, a method enabling high-throughput, spatially resolved profiling of thousands of operons within individual bacteria. Using bacterial-MERFISH, we dissect the response of E. coli to carbon starvation, systematically map subcellular RNA organization, and chart the adaptation of B. thetaiotaomicron to micron-scale niches in the mammalian colon. We envision bacterial-MERFISH could prove useful in the study of bacterial single-cell decisions made in diverse, spatially structured, and native environments.

2024-11-12 | GSE268480 | GEO

Amygdalostriatal transition zone neurons encode sustained valence to direct conditioned behaviors

Project description:The amygdalostriatal transition zone (ASt) is anatomically poised to provide a shortcut between corticolimbic and basal ganglia circuitry, and mediate behavioral responses to stimuli in parallel with the amygdala. Like the amygdala, the ASt receives converging sensory input from thalamic and cortical pathways. However, the projections of the ASt are distinct from canonical outputs of the amygdala complex, and are integrated with striatal circuits involved in action selection. Despite this intriguing circuit connectivity, the function of the ASt is almost completely unknown. In the present study, we collected cellular resolution recordings of genetically-defined neurons during a valence discrimination task to interrogate the functional role of ASt circuitry, and characterized the transcriptomic profile of the ASt in comparison to neighboring regions. We find that ASt neurons, and specifically, ASt neurons expressing dopamine receptor 2 (D2+), robustly encode sustained conditioned responses to cues of negative valence. Selective inhibition of D2+ ASt neurons was found to cause a striking reduction in conditioned fear responses. We also used single-nucleus RNA sequencing to generate a comprehensive profile of gene expression in ASt neurons, and found that the ASt is genetically distinct from adjacent GABAergic brain regions. RNAscope labelling also confirmed there is a greater proportion of D2+ neurons than D1+ neurons in the ASt, a unique feature compared to other regions of the striatum. Together, our findings provide the first evidence the ASt is a critical structure for encoding learned associations to direct motivated behavior.

2024-04-01 | GSE211437 | GEO

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