Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

PCR strategies for allele calling in multigene families using NGS.

ABSTRACT: PCR strategies for complete allele calling in multigene families using high-throughput sequencing approaches.

PROVIDER: PRJEB14070 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Rapid activation of distinct members of multigene families in Plasmodium spp.

Project description:Variant antigens that are encoded by large multigene families play an important role in the adaptation and immune evasion of a wide range of pathogens. However, the study of their biological function is significantly hampered by the difficulty in controlling their expression in its cellular setting. The genomes of Plasmodium spp. encode a number of different multigene families that are thought to play a critical role for their survival. However, with the exception of the P. falciparum var genes very little is known about the biological roles of any of the other multigene families. Here we report a highly efficient genetic system to study variant antigens in Plasmodium spp. using the Selection Linked Integration method; we are able to activate the expression of a single member of a multigene of our choice using its endogenous promoter.

2020-07-03 | GSE152162 | GEO

Rapid activation of distinct member of multigene families in Plasmodium spp.

Project description:The objective of this study is to provide a novel method to study multigene proteins in Plasmodium spp. The method is based on selection linked integration (SLI), which allows positive selection of genomic integration events. By targeting specific members of multigene families, parasites are being selected for not only genomic integration but also expression of the targeted gene under its endogenous promoter

2019-03-12 | GSE128123 | GEO

PCR Strategies for Complete Allele Calling in Multigene Families Using High-Throughput Sequencing Approaches.

Project description: Not available

| S-EPMC4905633 | biostudies-literature

Rapid activation of distinct member of multigene families in Plasmodium spp.

Project description:Rapid activation of distinct member of multigene families in Plasmodium spp.

| PRJNA526501 | ENA

Rapid activation of distinct members of multigene families in Plasmodium spp.

Project description:Rapid activation of distinct members of multigene families in Plasmodium spp.

| PRJNA638463 | ENA

Mutually Exclusive Transcription of Subtelomeric Gene Families in Plasmodium falciparum is Restricted to var Genes

Project description:The P. falciparum genome is equipped with several subtelomeric gene families that are implicated in parasite virulence and immune evasion. The members of these gene families are uniformly positioned within heterochromatic domains of the genome and are thus subject to variegated expression. The best-studied example is that of the var gene family encoding the major parasite virulence factor P. falciparum erythrocyte membrane protein 1 (PfEMP1). Transcriptional regulation of other subtelomeric gene families and their role in parasite biology is much less understood. Here, we investigated the mode of transcriptional control of var, rif, stevor, phist and pfmc-2tm families by comparative genome-wide transcriptional profiling of transgenic parasite lines. Our results establish a clear functional distinction between var and non-var transcriptional control mechanisms. Unlike var promoters, we find that promoters of non-var families are not silenced by default. Moreover, we show that mutually exclusive transcription is unique to the var gene family. 3D7 wild-type parasites were transfected with constructs carrying eight different promoters that drive expression of the drug-selectable marker hdhfr-gfp. Thereof seven promoters are members of the multigene families upsA var, upsB var, upsC var, rif, stevor, phistb and pfmc-2tm. The cam promoter was used as transfection-based control and also a wild-type 3D7 cell line was included as control. These nine cell lines were subjected to genome-wide transcriptional profiling. Parasites were synchronized to obtain an 8 hour growth window and were harvested at four consecutive timepoints (TP): TP1 (6-14 hours post-invasion (hpi)); TP2 (14-22 hpi); TP3 (22-30 hpi); TP4 (30-38 hpi) to monitor intra- and inter-family specific linkage of multigene family expression.

2011-09-01 | E-GEOD-31829 | biostudies-arrayexpress

Comprehensive transcriptome profiling reveals multigene signatures in triple negative breast cancer

2016-01-04 | GSE76250 | GEO

Comprehensive transcriptome profiling reveals multigene signatures in triple negative breast cancer

Project description:To develop and validate novel multigene signatures to facilitate individualized treatment of TNBC patients By integrating expression profiles of messenger RNAs (mRNAs) and long non-coding RNAs (lncRNAs). We analysed 165 TNBC samples and 33 paired normal breast tissues using transcriptome microarrays. Tumor-specific mRNAs and lncRNAs were identified and correlated with patientsâ?? recurrence-free survival (RFS). Using Cox regression model, we built two multigene signatures incorporating mRNAs and lncRNAs. The prognostic and predictive accuracy of the signatures were tested in a training set of 165 TNBC patients and validated in another 101 TNBC patients.

2016-01-04 | E-GEOD-76250 | biostudies-arrayexpress

Multigene biomarkers of pyrethroid exposure: preliminary experiments

Project description:Multigene biomarkers of pyrethroid exposure: preliminary experiments

| PRJNA450646 | ENA

GoPeaks: histone modification peak calling for CUT&Tag

Project description:Peak calling tool for CUT&Tag histone modifications.

2022-05-16 | GSE190793 | GEO