Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Caulanthus amplexicaulis var. barbarae

ABSTRACT: Caulanthus amplexicaulis var. barbarae Transcriptome or Gene expression

PROVIDER: PRJNA417949 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6281389_1.fastq.gz	Fastqsanger.gz
	SRR6281389_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Caulanthus amplexicaulis var. amplexicaulis

Project description:Caulanthus amplexicaulis var. amplexicaulis Transcriptome or Gene expression

| PRJNA417948 | ENA

Caulanthus amplexicaulis var. barbarae

Project description:Caulanthus amplexicaulis var. barbarae Genome sequencing

| PRJNA209542 | ENA

Project description:Caulanthus amplexicaulis var. amplexicaulis genomic DNA sequences

| PRJNA961164 | ENA

Project description:Caulanthus amplexicaulis var. barbarae genomic DNA sequences

| PRJNA954871 | ENA

Caulanthus amplexicaulis

Project description:Caulanthus amplexicaulis overview

| PRJNA209738 | ENA

Exploring the var gene interactome with CRISPR/dCas9

Project description:Epigenetic regulation of mutually exclusive transcription within the var gene family is important for infection and pathogenesis of the malaria parasite Plasmodium falciparum. var genes are kept transcriptionally silent via heterochromatic clusters located at the nuclear periphery; however, only a few proteins have been shown to play a direct role in var gene transcriptional regulation. Importantly, the chromatin components that contribute to var gene nuclear organization remain unknown. Here, we adapted a CRISPR-based immunoprecipitation-mass spectrometry approach for de novo identification of factors associated with specific transcriptional regulatory sequences of var genes. Tagged, catalytically inactive Cas9 (“dCas9”) was targeted to var gene promoters or introns, cross-linked, and immunoprecipitated with all DNA, proteins, and RNA associated with the targeted locus. Chromatin immunoprecipitation followed by sequencing demonstrated that genome-wide dCas9 binding was specific and robust. Proteomics analysis of dCas9-immunoprecipitates identified specific proteins for each target region, including known and novel factors such as DNA binding proteins, chromatin remodelers, and structural proteins. We also demonstrate the ability to immunoprecipitate RNA that is closely associated to the targeted locus. Our CRISPR/dCas9 study establishes a new tool for targeted purification of specific genomic loci and advances understanding of virulence gene regulation in the human malaria parasite.

2020-05-01 | GSE129397 | GEO

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.

2011-09-02 | GSE31829 | GEO

Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster

Project description:Histone modifications represent one of the key factors contributing to proper genome regulation. One of the histone modifications involved in gene silencing is H3K9 methylation, which is found in the chromosomes across different eukaryotes and controlled by SU(VAR)3-9 and its orthologs. Although SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern. To fill in this gap, we used DamID-seq approach and obtained high-resolution genome-wide profiles for SU(VAR)3-9 in two somatic and two germline tissues of fruitfly.

2017-04-04 | GSE97351 | GEO

Resin tapping transcriptome in adult slash pine (Pinus elliottii var. elliottii)

Project description:To better understand the molecular bases of resin production, a major source of terpenes for industry, the transcriptome of adult Pinus elliottii var. elliottii (slash pine) trees under field commercial resinosis was obtained.

2019-06-22 | GSE133168 | GEO

Genome-wide analysis of Su(var)3-9 distribution in chromosomes of Drosophila melanogaster [RNA-Seq_SuVar]

Project description:One of the histone modifications involved in gene silencing is H3K9 methylation, which is found in the chromosomes across different eukaryotes and controlled by SU(VAR)3-9 and its orthologs. Although SU(VAR)3-9 was discovered over two decades ago, little is known about the details of its chromosomal distribution pattern and effect on gene regulation during germ cells development. To fill in this gap, we used RNA-Seq approach to investigate the effect of Su(var)3-9 mutation on gene expression during Drosophila spermatogenesis.

2017-03-30 | GSE97130 | GEO

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