Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Blood borne pathogen detection in blood and plasma by Microarray

ABSTRACT: The Blood Borne Pathogen Resequencing Microarray Expanded (BBP-RMAv.2) is a platform that allows multiplex detection and identification of 80 different blood-borne pathogens in one single test, comprising 60 virus, 5 bacteria and 15 parasites. The objective is to evaluate the lowest concentration detected in blood or plasma, species discrimination and applicability of the microarray platform for testing blood donors. Human blood or plasma spiked with selected pathogens (10,000, 1,000 or 100 cells or copies/ml), including 6 viral, 2 bacterial and 5 protozoan pathogens were each tested on this platform. The nucleic acids were extracted, amplified using multiplexed sets of pooled specific primers, fragmented, labeled, and hybridized to a microarray. Finally, the detected sequences were identified using an automated genomic database alignment algorithm. The performance of the BBP-RMAv.2 demonstrated detection for most spiked protozoan pathogens at 1,000 cells/ml, 10,000 cells/ml for bacterial pathogens and as low as 100 copies/ml for viral pathogens. Coded specimens, including spiked and negative controls, were identified correctly for one blood specimen and for two plasma specimens. One negative plasma resulted in a false positive detection of a virus demonstrating the effectiveness of the platform.

INSTRUMENT(S): GeneChip Hybridization Oveer 640, Dell Precision Tower 7910 workstation, Bio-Rad T100 Thermocycler, Affymetrix GCS3000 7G SCANNER

ORGANISM(S): Babesia microti

SUBMITTER: Robert Duncan

PROVIDER: E-MTAB-13972 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

A genome-wide screen identifies silencers with distinct chromatin properties and mechanisms of repression

Project description:Differential gene transcription enables development and homeostasis in all animals and is regulated by two major classes of distal cis-regulatory DNA elements (CREs), enhancers and silencers. While enhancers have been thoroughly characterized, the properties and mechansisms of silencers remain largely unknown. By an unbiased genome-wide functional screen in Drosophila melanogaster S2 cells, we discover a class of silencers that bind one of three transcription factors (TFs) and are generally not included in chromatin-defined CRE catalogs, as they mostly lack detectable DNA accessibility. The silencer-binding TF CG11247, which we term Saft, safeguards cell fate decisions in vivo and functions via a highly-conserved domain we term ZAC and the corepressor G9a, independently of G9a’s H3K9-methyltransferase activity. Overall, our identification of silencers with unexpected properties and mechanisms has important implications for the understanding and future study of repressive CREs, as well as the functional annotation of animal genomes.

2024-11-13 | PXD048161 | Pride

Oxford Nanopore MinION sequencing of multiplex PCR amplified, pathogen-spiked blood and plasma samples

Project description:To evaluate targeted MinION next generation sequencing as a diagnostic method for detection of pathogens in human blood and plasma, human blood or plasma samples were spiked with measured amounts of viruses, bacteria, protozoan parasites or tested pathogen-free as negative controls. Nucleic acid was extracted from samples and PCR amplification performed in multiplex primer pools with a procedure described in ArrayExpress experiment submission ID 18379. The PCR products were used for library preparation. The libraries sequenced on an Oxford Nanopore MinION. The passed reads aligned with a custom reference file to determine the identity of the pathogen in the sample.

2024-06-08 | E-MTAB-14011 | biostudies-arrayexpress

Liver tissue HELP-tagging cytosine methylation data from C57BL/6J mice receiving high-fat diet with or without lingonberries

Project description:The C57BL/6J mouse model develops obesity and pre-diabetes when fed a high-fat diet. In this experiment, DNA methylation was assessed globally at specific CpG sites in liver tissue from mice receiving high-fat diet (45E% from fat) for 13 weeks (Control) or high-fat diet supplemented with 20% (w/w) of freeze-dried lingonberries (n=4). Our findings show that lingonberries prevent development of high-fat induced obesity, hepatic steatosis and low-grade inflammation, and the DNA was hypermethylated in mice receiving lingonberries compared to control. Genome wide hepatic DNA methylation comparison between mice fed high-fat diet with or without a lingonberry supplement (n=4/group).

2015-09-20 | E-GEOD-67277 | biostudies-arrayexpress

Tet1 is a tumor suppressor of hematopoietic malignancy

Project description:Epigenetic pathways that regulate DNA methylation and chromatin modifications are frequently found to be dysregulated in human cancers. The TET methylcytosine dioxygenase 1 (TET1) enzyme is an important regulator of hydroxymethylcytosine (5hmC) in embryonic stem cells, neural progenitors,adult cells and reprogrammed cells. Decreased expression of TET proteins and loss of 5hmC has been reported in many tumors, suggesting a critical role for the maintenance of this epigenetic modification in normal cellular function. However, loss of TET1 function in the etiology of cancer has not been directly investigated. Here, we show that deletion of the Tet1 gene promotes the development of B cell lymphoma. Tet1 is required for maintaining normal levels of 5hmC, preventing aberrant DNA hypermethylation and for the regulation of transcriptional programs involved in B-cell lineage specification, chromosome maintenance, and DNA repair. Progenitor B cells in the absence of Tet1 accumulate DNA damage and whole-exome sequencing of Tet1-deficient tumors revealed a high correlation of mutations with those most frequently found in Non-Hodgkin B cell lymphoma (B-NHL) patients. In addition, we show that the TET1 gene is deleted, hypermethylated and transcriptionally silenced in B-NHL patients. These findings provide the first in vivo evidence of TET1 function as a tumor suppressor of hematopoietic malignancy. We did hydroxymethylation tests for two wild type mice and two Tet1 knockout mice.

2015-04-12 | E-GEOD-65895 | biostudies-arrayexpress

Single-base resolution DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi, by whole-genome bisulfite sequencing (MethylC-seq).

Project description:Here we provided the first single-base resolution DNA methylatome in chicken lungs by whole-genome bisulfite sequencing (MethylC-seq). In addition, two genetically distinct highly inbred chicken lines, Leghorn and Fayoumi, were used to examine how DNA methylation regulates mRNA gene expression between two lines. The methylation profile demonstrated that methylcytosines in the chicken were more likely to occur in CG dinucleotides than in non-CG sites. DNA methylation in the gene body region, especially in the internal exons, was higher than in the 5’ and 3’ flanking regions of genes.Differentially methylated region (DMR) analysis indicated widespread differences between the Leghorn and Fayoumi lines. Of particular interest, many identified DMR-associated genes were significantly enriched in immune-related groups, which indicate that DNA methylation may regulate host immune response to pathogen infection in chickens as these two genetic lines have demonstrated differential resistance to a few pathogens. This work establishes a comprehensive and precise DNA methylation pattern in chickens and lays a solid foundation for future studies on epigenetic modifications related to poultry growth, disease, and development. DNA methylation profiles of two highly inbred chicken lines, Leghorn and Fayoumi,which were generated by deep sequencing, using Illumina GAII

2015-06-28 | E-GEOD-56975 | biostudies-arrayexpress

Tracking Ebolavirus genomic drift with a resequencing microarray

Project description:This study evaluates a resequencing microarray designed to determine the sequence of the four major genes in the Ebolavirus genome, Nucleoprotein (NP), matrix protein (VP40), glycoprotein (GP) and polymerase (L). The array has the ability to determine the sequence of five species and strains: Zaire Ebolavirus (Mayinga and Makona), Bundibugyo Ebolavirus, Sudan Ebolavirus and Tai Forest Ebolavirus.

2021-01-29 | E-MTAB-10007 | biostudies-arrayexpress

Genome-wide Chromatin Maps Derived from Limited Numbers of Hematopoietic Progenitors

Project description:Whole genome mapping of protein-DNA interactions can be performed by coupling chromatin immunoprecipitation (ChIP) with high-throughput sequencing (ChIP-Seq). However, current methods require large amounts of starting materials which precludes their application to rare cell types. Here, we combine a high-sensitivity ChIP assay with a novel library preparation procedure to map histone modifications in as few as 10,000 cells. We apply the technique to acquire genome-wide chromatin maps for an enriched population of hematopoietic progenitors, and thereby gain insight into their developmental program. An optimized ChIP protocol for small number of cells and a novel Librray preperation methods for high throughput sequencing of picograms amount of ChIP DNA.

2010-07-01 | E-GEOD-22075 | biostudies-arrayexpress

Identification of thalidomide modulation related genes in mesenchymal stem cells

Project description:Comparison of gene expression data from thalidomide modulated- and unmodulated-MSCs from patients with idiopathic thrombocytopenic purpura (ITP). This experiment consists of 3 arrays.

2013-03-12 | E-GEOD-44948 | biostudies-arrayexpress

A Structure-Based Mechanism for DNA Entry into the Cohesin Ring

Project description:The ring-shaped cohesin complex is thought to fulfil its roles in sister chromatid cohesion, genome stability and gene regulation by topologically encircling DNAs. The ring is formed by two Structural Maintenance of Chromosome (SMC) subunits, whose ATPase heads are linked by a kleisin subunit. Additional components, including the Mis4Scc2/NIPL cohesin loader, engage the kleisin. Here, we visualize a DNA gripping intermediate during cohesin loading onto DNA by cryo-electron microscopy. ATP-dependent head engagement creates an interaction surface onto which Mis4Scc2/NIPL clamps the DNA. We use biophysical tools to establish the order of events during cohesin loading. DNA first traverses an N-terminal kleisin gate that was opened by ATP binding and closed again as the loader locks the DNA. Ensuing ATP hydrolysis and head disengagement, assisted by Mis4Scc2/NIPL, will complete DNA entry. A conserved kleisin N-terminal tail guides the DNA on its trajectory to successful topological DNA entry into the cohesin ring.

2020-08-05 | PXD018600 | Pride

Parity and the genomic signature in the Human Breast

Project description:Case-control study for the analysis of the gene expression profile of epithelial cells microdissected from normal breast tissues obtained from 17 parous and 7 nulliparous women free of breast pathology (controls), and 39 parous and 8 nulliparous women with history of breast cancer (cases). Keywords: genetic modifications Four-condition experiment: nulliparous case, nulliparous control, parous case and parous control labeled with Cy5 and Universal human reference used as a common reference labeled with Cy3. Moderated t statistic was used as the basic statistic for significance analysis; it was computed for each probe and for each contrast. False discovery rate was controlled using the Benjamini and Hochberg. All genes with P value below a threshold of 0.05 were selected as differentially expressed, maintaining the proportion of false discoveries in the selected group below the threshold value, in this case 5%. Breast 11 parous control HuII, Breast 28 parous case HuII, and Breast 62 nulliparous control HuIII excluded: raw data is missing

2008-11-03 | E-GEOD-13293 | 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