Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome of chicken spleens with Escherichia coli infection

ABSTRACT: Transcriptome of chicken spleens with Escherichia coli infection

PROVIDER: PRJNA758443 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR15660419_1.fastq.gz	Fastqsanger.gz
	SRR15660419_2.fastq.gz	Fastqsanger.gz
	SRR15660420_1.fastq.gz	Fastqsanger.gz
	SRR15660420_2.fastq.gz	Fastqsanger.gz
	SRR15660421_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 40

Similar Datasets

Transcriptome of chicken spleens with Escherichia coli infection

Project description:Purpose: the goals of this study was to find the differential genes of spleen in chickens infected with Escherichia coli Methods: The spleen samples from control group and the spleen samples from infection group were generated by deep sequencing using Illumina system with 9 biological repetitions and 2 technical repetitions, respectively. Results: Using an optimized data analysis workflow, we mapped about 68-91 million sequence reads per sample to the chicken spleens from the infection and control group by Hisat2. Approximately a quarter of the transcripts showed differential expression between the infection and control group, with a 5x SD fold change and p value <0.05.

2023-01-11 | GSE182967 | GEO

Transcriptome analysis of avian pathogenic Escherichia coli O1 in chicken serum compared to LB

Project description:Colisepticemia caused by avian pathogenic Escherichia coli (APEC) results in annual multimillion dollar losses to the poultry industry. Recent research suggests that APEC may have an important role in public health as well. Generally, colisepticemia follows a respiratory tract infection in which APEC penetrate the respiratory epithelium to enter the bloodstream. From the bloodstream, bacteria may spread to various internal organs resulting in perihepatitis, pericarditis, and other conditions. The aim of this study was to identify molecular mechanisms enabling APEC to survive and grow in the bloodstream. To do so, we compared the transcriptome of APEC O1 during growth in Luria-Bertani broth and chicken serum. Selected genes that were significantly up-regulated in chicken serum were then subjected to mutational analysis to confirm their role in APEC pathogenesis. Several categories of genes, predicted to contribute to adaptation and growth in the avian host, were identified. These included several known virulence genes and genes involved in adaptive metabolism, protein transport, biosynthesis pathways, stress resistance, and virulence regulation. Several genes with unknown function, which were localized to pathogenicity islands or APEC O1’s large virulence plasmid, were also identified, suggesting that they too contribute to survival in chicken serum. This genome-wide analysis provides novel insight into processes that are essential to APEC O1’s survival and growth in chicken serum.

2011-04-01 | GSE25478 | GEO

Transcriptome analysis of avian pathogenic Escherichia coli O1 in chicken serum compared to LB

2011-03-31 | E-GEOD-25478 | biostudies-arrayexpress

DNA microarray-mediated transcriptional profiling of avian pathogenic Escherichia coli O2 strain E058 during its infection of chicken

Project description:APEC most often infect chickens, turkeys, ducks, and other avian species, and therefore pose a significant economic burden on the poultry industry worldwide. Few studies have analyzed the genome-wide transcriptional profile of APEC during infection in vivo. In this study, we examined the genome-wide transcriptional response of APEC O2 strain E058 in an in vivo chicken infection model to better understand the factors necessary for APEC colonization, growth, and survival in vivo. An Affymetrix multigenome DNA microarray, which contains most of the genomic open reading frames of E. coli K-12 strain MG1655, uropathogenic E. coli strain CFT073, and E. coli O157:H7 strain EDL 933, was used to profile the gene expression in APEC E058.The genes highly expressed during infection were involved in metabolism, iron acquisition or transport, virulence, response to stress, and biological regulation. Many genes encoding putative or hypothetical proteins were also strongly upregulated, implying that some undiscovered mechanism may underlie APEC pathogenesis.

2016-05-28 | GSE81974 | GEO

Escherichia coli strain:chicken | isolate:chicken

Project description:Escherichia coli strain:chicken | isolate:chicken Raw sequence reads

| PRJNA764072 | ENA

RNA-seq of chicken spleens after LPS injection

Project description:RNA-seq of chicken spleens after LPS injection

| PRJEB28060 | ENA

Response to Avian Pathogenic Escherichia coli (APEC) Infection in diverse chicken tissues

Project description:Response to Avian Pathogenic Escherichia coli (APEC) Infection in diverse chicken tissues

| PRJNA284292 | ENA

Genome-wide studies of microRNAs in Marek's tumorigenesis in Chicken (miRNA-Seq)

Project description:Marek's disease (MD), induced by Marek's disease virus (MDV), is a lymphotropic neoplastic disease and causes huge economic losses to the poultry industry. Non-coding RNAs play important regulatory roles in disease pathogenesis. To investigate host miRNA expression profile, RNA sequencing was performed in tumorous spleens (TS), spleens from the survivors (SS) without any lesion after MDV infection, and noninfected chicken spleens (NS).

2020-01-21 | GSE138601 | GEO

Transcriptomic analyses of co-infection of Mycoplasma gallisepticum and Escherichia coli in chicken lungs

Project description:Purpose:In order to assess the respiratory toxicity of co-infection in chicken lung, we established a co-infection model to investigate transcriptome profiles of chicken lung. Methods: RNA extracted by Trizol reagent (Invitrogen) was utilized to construct the final library (BGISEQ-500 RNA-Seq Library) based on the manufacturer’s instructions. Library was validated on the Agilent Technologies 2100 bioanalyzer. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were load into the patterned nanoarray and single end 50 bases reads were generated in the way of sequenced by synthesis. Whole transcriptome sequencing data was filtered and mapped to Chicken genome (Gallus genome Version 5.0.1 NCBI). DEG-seq method was based on Poisson distribution (Fold Change > 2 and Adjusted P value < 0.001) Results: Sampling directly from the lung yielded sufficient quantities of RNA to assess transcripts from each chicken and mapped to 18,043 Gallus gallus genes. Conclusions: We used the method of RNA-seq to find the target genes and related signaling pathways involved in the co-infection (MG and E.coli) and their underlying mechanisms.

2019-04-19 | GSE130015 | GEO

Psychological Evaluation According Colonic Colonization by Escherichia Coli of Patients After Colorectal Surgery

Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.

| 2230352 | ecrin-mdr-crc

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