Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

17 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

BIGenomics_hpv_dilution_series

ABSTRACT: A dilution series experiment to determine the sensitivity of a microarray method for human papillomavirus genotyping. HPV genotyping is based on multiplex PCR (PGMY-t primers) followed by ligation step where two probes are ligated together if a matching template is present in the mixture. The ligated probes are then detected on microarray. Plasmids containing the full genome of HPV 16 or 18 were used in the experiment. The concentrations were 1000, 100, 10 ,1, 0.1 and 0 femtograms of plasmid as a template in HPV PCR reaction.

ORGANISM(S): Human papillomavirus

SUBMITTER: Jarmo Ritari

PROVIDER: E-MEXP-3477 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

BIGenomics HPV zipcode array plasmid hybridizations

Project description:Hybridization of HPV genotype recognizing ligation probes to a zipcode (tag) microarray. The purpose of the experiment is to establish functionality and target specificity of the ligation probes by using a single template at a time with all of the probes. HPV plasmid DNA PCR products are used as templates for ligation probes. Each plasmid contains the full genome of a given HPV type. One type of plasmid is used per experiment to test the signals of all of the probes agains that template. 19 different plasmids are tested this way (i.e. 19 samples in the experiment).

2011-06-01 | E-MEXP-3152 | biostudies-arrayexpress

BIGenomics HPV zipcode array multiplex PCR tests

Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 1 ng or 1 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.

2011-05-01 | E-MEXP-3154 | biostudies-arrayexpress

BIGenomics HPV zipcode array multiplex PCR tests 2

Project description:Comparison of two different multiplex PCR primer pools in amplifying target HPV types from plasmid templates. Template concentrations are either 10 pg or 100 pg. Templates are detected by type-spcific LDR probes hybridized on microarray.

2011-08-20 | E-MEXP-3268 | biostudies-arrayexpress

BIGenomics HPV zipcode array multiple plasmid hybridizations

Project description:Replicates of detection of multiple plasmid PCR products by LDR probes on microarray.

2011-05-01 | E-MEXP-3153 | biostudies-arrayexpress

BIGenomics HPV zipcode array patient sample hybridizations

Project description:HPV genotyping of patient samples by multiplex PCR (PGMY-t primers) and ligation detection probes on microarray.

2011-05-01 | E-MEXP-3155 | biostudies-arrayexpress

BIGenomics_hpv_Agilent

Project description:Human papillomavirus infection is the cause of essentially all cases of cervical premalignant lesions and cervical cancer. Primary screening using HPV DNA testing with cytology triage has been shown to be more sensitive and, importantly, more specific than conventional testing based on cytology among women more than 35 years of age. <br><br><br><br>The aim of the experiment was to evaluate a HPV genotyping microarray method using patient sample DNA. HPV genotyping is based on multiplex PCR (PGMY-t primers) followed by ligation step where two probes are ligated together if a matching template is present in the mixture. The ligated probes are then detected on microarray.

2011-12-10 | E-MEXP-3466 | biostudies-arrayexpress

BIGenomics_Agilent_15k_templates

Project description:Hybridization of ligation probes to a zipcode (tag) microarray. The purpose of the experiment was to establish functionality and target specificity of the ligation probes by using pools of synthetic templates with all of the probes. The templates are 80-mer synthetic dsDNA molecules, each specific for a single probe. Each probe is a ssDNA molecule containing target recognition sequences, PCR primer binding sequences and a unique tag sequence. If a matching target sequence is present in the mixture, the probes is ligated into a circular molecule, which can be PCR amplified and hybrized on a microarray harbouring complementary tag sequences.

2012-02-24 | E-MEXP-3538 | biostudies-arrayexpress

BIGenomics_bioreactor_sensitivity

Project description:Ligation probe pool was tested with different concentrations of synthetic dsDNA template molecules to determine analytical sensitivity of the method. Probes are ligated into circular molecules if their target sequence is present in the reaction. Ligated probes are then PCR amplified and the PCR products are hybridized to a microarray by tag sequences.

2012-02-06 | E-MEXP-3539 | biostudies-arrayexpress

BIGenomics_bioreactor_samples

Project description:The aim of the study was to use microarray for profiling the microbiota in anaerobic digestion process. The probes are ssDNA molecules that are ligated into circular molecules if a complementary target sequence is present in the sample DNA. Ligated probes are PCR amplified with a labeled primer, and the amplicons are hybridized on DNA microarray by tag sequences.

2012-02-06 | E-MEXP-3541 | biostudies-arrayexpress

A ubiquitin variant-based affinity approach selectively identifies substrates of the ubiquitin ligase E6AP in complex with HPV-11 E6 or HPV-16 E6

Project description:The E6 protein of both mucosal high risk human papillomaviruses (HPVs) such as HPV-16, which have been causally associated with malignant tumors, and low risk HPVs such as HPV-11, which cause the development of benign tumors, interacts with the cellular E3 ubiquitin ligase E6AP. This indicates that both HPV types employ E6AP to organize the cellular proteome to viral needs. However, while several substrate proteins of the high risk E6-E6AP complex are known, e.g. the tumor suppressor p53, potential substrates of the low risk E6-E6AP complex remain largely elusive. Here, we report on an affinity-based enrichment approach that enables the targeted identification of potential substrate proteins of the different E6-E6AP complexes by a combination of E3-selective ubiquitination in whole cell extracts and high-resolution mass spectrometry. The basis for the selectivity of this approach is the use of a ubiquitin variant that is efficiently used by the E6-E6AP complexes for ubiquitination, but not by E6AP alone. By this approach, we identified approximately 190 potential substrate proteins for low risk HPV-11 E6 as well as high risk HPV-16 E6. Moreover, subsequent validation experiments in vitro and within cells with selected substrate proteins demonstrate the potential of our approach. In conclusion, our data represent a reliable repository for potential substrates of the HPV-16 and HPV-11 E6 proteins in complex with E6AP.

2020-08-31 | PXD020660 | Pride

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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