Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Improving Food Security in Africa by Enhancing Resistance to Newcastle Disease and Heat Stress in Chickens

ABSTRACT: The program is to utilize the cutting-edge genomic technologies enhance innate resistance to Newcastle disease in chickens adapted to the African environment, thereby increasing food security, nutrition, and livelihoods in Africa -- key goals of the United States Agency of International Development Feed the Future Program.

INSTRUMENT(S): -

ORGANISM(S): Gallus Gallus Gallus

SUBMITTER: Feed the Future Innovation Lab for Genomics to Improve Poultry

PROVIDER: PRJEB39468 | EVA | 2020-07-21

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Similar Datasets

Ex vivo P. falciparum from High vs Low transmission areas in east Africa

Project description:The aim of this study was to compare the transcriptomes of Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment. In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and measured for gene expression levels by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Rono MK, Nyonda MA, Simam JJ, Ngoi, JM et al. Nat Ecol Evol. PMID: .

2017-12-18 | GSE108034 | GEO

Copy number variation in ex vivo P. falciparum from High vs Low transmission areas in east Africa

Project description:The aim of this study was to describe gene copy number variation in Plasmodium falciparum parasites sourced from high vs. low malaria transmission settings in east Africa in order to test the hypothesis that malaria parasites are locally adapted to their environment. In three separate experiments, parasites from ‘High’ vs. ‘Low’ transmission populations were taken from non-immune children and evaluated for copy number variants by microarray against a reference genome. Two of these population comparisons were geographic in nature while the third was temporal, i.e., before and after a marked decline in malaria. This study is described in Simam et al. 2018 BMC Genomics.

2018-05-30 | GSE113087 | GEO

Transcriptional rearrangements associated with thermal stress and preadaptation in Baikal whitefish (Coregonus baicalensis)

Project description:In this work, we describe the transcriptional profiles of adapted and non-adapted one-month-old Baikal whitefish juveniles after heat shock exposure. Preadapted fish were exposed to a repeated thermal rise of 6 °C above control temperature every 3 days throughout embryonic development. One month after hatching, preadapted and non-adapted larvae were either maintained at control temperatures (12 °C) or exposed to an acute thermal stress (TS) of 12 °C above control temperature. The information on transcriptional profiles will contribute to further understanding of the mechanisms of adaptation of whitefish to the environment.

2024-10-15 | GSE278874 | GEO

Aging Promotes Metabolic Dysfunction-associated Steatotic Liver Disease and Multi-Organ Dysfunction by Inducing Ferroptotic Stress

Project description:Aging is an inevitable consequence of living that undermines cellular resiliency to cause tissue degeneration and eventual multi-organ dysfunction. Susceptibility to biological consequences of aging varies among organs and individuals. Stressors that challenge resiliency unmask these differences. Hence, aging increases the risk for failure of many metabolically-stressed organs and exacerbates liver degeneration related to obesity and diabetes. We discovered that aging promotes ferroptosis, a type of metabolism-regulated cell death, in hepatocytes. Hepatocytes that have launched the ferroptotic death program adapt their metabolism to survive but become damaged and dysfunctional. Metabolic stressors amplify this, increasing the burden of ferroptosis-adapted cells and liver damage. Blocking ferroptotic signaling in old livers reduces accumulation of adapted hepatocytes and reverts livers to a more youthful resilient state despite exogenous stressors. Ferroptosis is also induced in other organs that are damaged by chronic metabolic stress, identifying ferroptosis as a tractable conserved mechanism for aging-related multi-organ dysfunction.

2024-07-01 | GSE262457 | GEO

Longer read lengths are required for RNA velocity analysis of single-cell RNA-sequencing with paired immune repertoire and transcriptome profiling

Project description:Increasing numbers of studies utilize single cell sequencing (scSeq) technologies that are capable of simultaneously profiling T/B-cell receptor (TCR/BCR) sequences and RNA expression. Here we show that standard sequencing of commonly-used 5’-biased scSeq chemistry precludes the ability to perform RNA velocity analysis; however extended sequencing lengths that allow for paired-end genome alignment alleviates these issues. This study provides important practical implications for paired TCR/BCR and RNA scSeq experiments.

2022-03-25 | GSE169657 | GEO

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station

2016-03-31 | GSE74708 | GEO

Transfer RNAs mediate rapid adaptation of Escherichia coli under oxidative stress

Project description:We performed tRNAome sequencing to assess the tRNA changes of E.coli under oxidative stress. We found that the global translation inhibition is caused by global down-regulation of almost all tRNA species under oxidative stress. The translation elongation speed is resumed after the cells are fully adapted to the oxidative environment.

2015-05-28 | GSE62995 | GEO

Adaptive evolution of Corynebacterium glutamicum resistant to oxidative stress and its global gene expression profiling

Project description:Corynebacterium glutamicum was adapted in a chemostat for 1,900 h with gradually increasing H2O2 stress to understand the oxidative stress response of an industrial host. After 411 generations of adaptation, C. glutamicum developed the ability to grow under stress of 10 mM H2O2, whereas the wild-type did not. The adapted strain also showed increased stress resistance to diamide and menadione, SDS, Tween 20, HCl, NaOH, and ampicillin. A total of 1,180 genes in the RNA-seq transcriptome analysis of the adapted strain were up-regulated twice or higher (corresponding to 38.6 % of the genome), and 126 genes were down-regulated half or less (4.1 % of genome) under 10 mM H2O2-stress conditions compared with those of the wild-type under a no stress condition. Especially the aromatic compound-degrading gene clusters (vanRABK, pcaJIRFLO, and benABCDRKE) were more than threefold up-regulated. Plausible reasons for the H2O2-stress tolerance of the adapted strain are discussed as well as the potential strategy for development of oxidative stress-tolerant strain. Comparison of global gene expression profiling using RNA-seq data of wild-type strain under normal condition (WT_MCGC) vs. 10 mM H2O2-adapted strain under oxidative stress condition Global gene expression profiling_WT vs. H2O2 adapted C. glutamicum strains

2013-01-06 | E-GEOD-41232 | biostudies-arrayexpress

Effects of a Closed Space Environment on Gene Expression in Hair Follicles of Astronauts in the International Space Station

Project description:In recent times, long-term stay has become a common occurrence in the International Space Station (ISS). However, adaptation to the space environment can sometimes pose physiological problems to the astronauts after their return. Therefore, it is important to develop healthcare technologies for astronauts. In this study, hair, an easy-to-obtain sample, was identified as the candidate. In order to investigate the genetic changes in human hair during space flight, the hair follicles of 10 astronauts were analyzed by DNA microarray and real time q-PCR analyses. Space environment induced gene expression of hair follicles of astronaut was measured 6 differnent times included 2 in flight on orbit. Ten independent experiments were performed on differing astronauts. and the sampling day was differed for each astronaut because of their schedules.

2016-03-31 | E-GEOD-74708 | biostudies-arrayexpress

Acute lung injury results from innate sensing of viruses by an ER stress pathway

Project description:Incursions of new pathogenic viruses into humans from animal reservoirs are occurring with alarming frequency. The molecular underpinnings of immune recognition, host responses, and pathogenesis in this setting arepoorly understood. We studied pandemic influenza viruses to determine the mechanism by which increasing glycosylation during evolution of surface proteins facilitates diminished pathogenicity in adapted viruses. ER stressduring infection with poorly glycosylated pandemic strains activated the unfolded protein response, leading to inflammation, acute lung injury, and mortality. Seasonal strains or viruses engineered to mimic adapted viruses displaying excess glycans on the hemagglutinin did not cause ER stress, allowing preservation of the lungs and survival. We propose that ER stress resultingfrom recognition of non-adapted viruses is utilized to discriminate “non-self” at the level of protein-processing and to activate immune responses, with unintended consequences on pathogenesis. Understanding this mechanism should improve strategies for treating acute lung injury from zoonotic viral infections. Lung transcription analysis of Influenza A virus infected mice.

2015-07-06 | E-GEOD-65075 | 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