Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sustainable Small Ruminant Production through Selection for Resistance to Internal Parasites (goat)

ABSTRACT: Animals used in the study belong to from four commercial farms and Langston University, born between 2013 and 2015. A total number of one hundred and forty four goats were genotyped with Capture Sequencing (Rapid Genomics, Gainesville, FL). The samples correspond to Boer, Kiko and Spanish goats.

INSTRUMENT(S): -

ORGANISM(S): Capra Hircus

SUBMITTER: University of Florida, Department of Animal Sciences

PROVIDER: PRJEB32312 | EVA | 2019-06-11

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	goatdata.accessioned.vcf.gz	Vcf
	goatdata.vcf.gz	Vcf
	goatdata.vcf.gz.tbi	Vcf

Items per page:

1 - 3 of 3

Similar Datasets

Sustainable Small Ruminant Production through Selection for Resistance to Internal Parasites (sheep)

Project description:Animals used in the study belong to from four commercial farms and Langston University, born between 2013 and 2015. A total number of one hundred and forty four sheep were genotyped with Capture Sequencing (Rapid Genomics, Gainesville, FL). The first 47 samples correspond to Dorper sheep. Then the next 57 samples correspond to Katahdin sheep. Finally, the last 40 samples correspond to St. Croix sheep.

2019-06-11 | PRJEB32310 | EVA

Genetic Markers for Resistance to Gastrointestinal Nematode Infections for a Sustainable Florida Native Sheep Production

Project description:Animals used in the study belong to on commercial farm of Florida Native sheep located in Ocala, Florida. A total number of one hundred Florida Native sheep were genotyped with Capture Sequencing (Rapid Genomics, Gainesville, FL) and SNP data were derived from sequencing results.

2019-06-11 | PRJEB32462 | EVA

Project description:Ruminant H57 Feeding Trial 2013-2015

| PRJNA419525 | ENA

Transcriptome analysis revealed the characteristics and functions of long non-coding RNAs in the hypothalamus during sexual maturation in goats

Project description:To reveal the transcriptomic changes of hypothalamic tissue in goats from birth to sexual maturity, we performed transcriptome sequencing of Jining Grey Goat hypothalamic tissues at four developmental stages after birth. A total of 20 libraries from four different development stages (5 goats per stage) were successfully constructed, and the corresponding mRNA and lncRNA expression profile were obtained.

2024-06-01 | GSE244004 | GEO

Lignin production associated genes in Cenchrus purpueus

Project description:This study aims to reveal genes related to lignin production in Cenchrus purpureus through RNA-Seq. This species is widely used as forrage for cattle, and for the last years, due to its high biomass yield, has been considered as source to lignocellulosic ethanol. Given those two importances, lignin is a molecule related to low digestibility in cattle and recalcitrance in biofuel production. Eight samples were chosen from previous lignin production and forage quality data; four samples had low lignin production, and four had high lignin production. The highest nodes were collected for RNA extraction using TRIzol reagent, following Jordon-Thaden et a;. (2015) protocol. The cDNA library preparation was generated according to Illumina TruSeq Stranded mRNA Sample Prep kit protocol, and RNA sequencing was performed using HiSeq 2500 sequencer. Quality control was measured by FastQC software v 0.11.8. The sequenced reads were aligned to Cenchrus purpureus genome through STAR software v. 2.5.2b (Dobin et al., 2012). After that, the transcriptome was assembled using Stringtie v 2.0.4 software (Pertea et al., 2015). Salmon v 0.7.2 software (Patro et al., 2017) was used to quantify the sequenced reads. The DEG was identified using DESeq2 package, and genes functions were annotated through Trinotate software (Bryant et al., 2017). In total, approximately 130 million reads were sequenced. The final assembled transcriptome was formed by 101,169 transcripts. The differential expressed genes analysis revealed 52 significatively genes. Here, we highlighted genes related to sterol, L-serine and terpene biosynthetic process.

2021-10-01 | GSE174718 | GEO

Differentially Expressed LncRNAs Might be Controlling Signaling Pathways by Establishing Interactions with mRNAs and MicroRNAs in Pediatric Astrocytoma

Project description:In this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The Affymetrix HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively. A total of seven astrocytic tumors and two control tissues were collected during the period of 2012–2014: four low-grade Ast (three pilocytic Ast (PAst) and one diffuse Ast (DAst)) and four high-grade Ast (four glioblastoma multiforme (GBM)).RNA was extracted from tissue samples using TRIzol (Ambion life technologies, Thermo Scientific Inc.) following the methodology described by Hongbao et al. 2008 and with certain modifications described by Vujovic et al. 2013. For expression analysis, Human Transcriptome Array 2.0 (HTA) (Santa Clara, CA, USA) was employed. in this study was determined the global expression pattern of long non-coding RNAs, mRNAs, and miRNAs in pediatric astrocytoma of different histological grades. The HTA 2.0 array showed expression changes on one hundred-sixty two and two hundred-fifteen long non-coding RNAs in tumors (versus the control) and in GBM (versus low-grade astrocytoma), respectively.

2015-08-25 | E-GEOD-72269 | biostudies-arrayexpress

Clostridium thermocellum Transcriptomic Profiles after Exposure to Furfural or Heat Stress

Project description:Background: The thermophilic anaerobe Clostridium thermocellum is a candidate consolidated bioprocessing (CBP) biocatalyst for cellulosic ethanol production. It is capable of both cellulose solubilization and its fermentation to produce lignocellulosic ethanol. Intolerance to stresses routinely encountered during industrial fermentations may hinder the commercial development of this organism. Results: In this study, C. thermocellum was grown to mid-exponential phase and treated with furfural or heat to a final concentration of 3 g.L-1 or 68°C respectively to investigate physiological and regulatory responses. Samples were taken at 10, 30, 60 and 120 min post-shock, and from untreated control fermentations, for transcriptomic analyses and selected extracellular metabolite determinations and compared to a published dataset from an ethanol stress study. In total 1,474 genes were differentially expressed significantly in at least a single time point for a given stressor. One hundred and forty three common genes were differentially expressed for heat, furfural and ethanol stressors including up-regulated genes encoding DNA repair enzymes, Hsp20, sulfate transporter subunits and enzymes in the sulfate assimilatory pathway. Conclusions: This study has identified C. thermocellum gene regulatory motifs and aspects of physiology and gene regulation for further study. The nexus between future systems biology studies and recently developed genetic tools for C. thermocellum offers the potential for more rapid strain development and for broader insights into this organism’s physiology and regulation.

2013-01-01 | GSE40402 | GEO

Shotgun proteomic profiling of Yersinia ruckeri strains

Project description:Project goal is to identify proteomic profiles of Yersinia ruckeri, the causative agent of enteric redmouth disease in fish. Four strains (SP-05, CSF007-82, 7959-11 and YRNC-10) of Y. ruckeri were isolated from disease rainbow trout, Oncorhynchus mykiss. Strains, SP-05 and CSF007-82, belong to serotype 1 and biotype 1 (motile and lipase positive), while strains 7959-11 and YRNC-10 belong to serotype 1 and biotype 2 (non-motile and lipase negative) and belong to serotype 1. A single colony of each strain was inoculated into tryptic soy broth (Casein peptone, dipotassium hydrogen phosphate, glucose, sodium chloride, soya peptone, Sigma) and grown at 22 °C with shaking (150 rpm). These starter cultures were then diluted with fresh sterile tryptic soy broth to an optical density (OD 600) of 0.10 ± 0.05. Five hundred microlitres of the diluted starter cultures were inoculated in duplicates, into 25 ml of tryptic soy broth. Cultures were grown overnight at 22 °C with shaking (150 rpm) until the late log phase. Cells were harvested by centrifugation, then washed three times with PBS.

2017-09-22 | PXD005439 | Pride

Comprehensive proteome profiling of a Xanthomonas campestris pv campestris B100 culture grown in a minimal medium with a specific focus on nutrient consumption and xanthan biosynthesis

Project description:Xanthan is the most used polysaccharide of bacterial origin. There are many industrial applications for xanthan, especially in food products. The organism Xanthomonas campestris is commonly used for xanthan fermentation, but little is known about the xanthan synthesis mechanism on the proteome level. The study used a label-free LC-MS/MS method to investigate the protein shifts during a typical xanthan fermentation of 72 hours. Two thousand four hundred sixteen proteins were identified, representing 54.75 % of the 4413 entries in the reference database. One thousand seven hundred forty-nine proteins were measured in a quantifiable quality. The quality of the proteome data was examined by the abundance changes of the ribosomal proteins according to the growth phases. The phenotypic changes during the cultivation, especially processes known to be influencing or close related to xanthan production, were investigated by proteome analysis. These processes were nitrogen metabolism, sugar nucleotide metabolism, and xanthan synthesis. This study shows the abundance of changes in central metabolites during a xanthan fermentation of Xcc. The presented research provides crucial information for further biotechnological studies to improve xanthan production.

2024-05-24 | PXD041470 | Pride

MS Versus NICE for Colorectal Lesions

Project description:OBJECTIVE: Our study aimed to compare a recently-developed endoscopic classification with an established one for colorectal lesions in a randomised trial between 2013 and 2015.

| 2229791 | 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