Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Silver birch genome sequencing

ABSTRACT: Genome sequencing and population genomics of silver birch (Betula Pendula)

PROVIDER: PRJEB14544 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	ERR1990240.fastq.gz	Fastqsanger.gz
	ERR1990250.fastq.gz	Fastqsanger.gz
	ERR1990241.fastq.gz	Fastqsanger.gz
	ERR1990251.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 299

Similar Datasets

silver birch succession

Project description:silver birch succession Metagenomic assembly

| PRJNA832321 | ENA

Transcription profiling of ethylene-dependent responses to short day exposure in birch apices

Project description:We have used transgenic ethylene-insensitive birches (Betula pendula), which express the Arabidopsis ethylene receptor gene ETR1 carrying the dominant mutation etr1-1, to investigate the role of ethylene in short day (SD) -induced responses in the shoot apical meristem in birch. Wild-type birch (clone V5834) and two ethylene-insensitive lines in this background (BPetr1-1-35 and BPetr1-1-86; see Plant Physiol 132: 185-195) were exposed to SD. After 12, 16 and 20 days under SD, apices of branches of three trees were pooled before RNA extraction from each sample. To study the ethylene-dependent SD-transcriptome in birch apices, the RNA extracts of lines BPetr1-1-35 and BPetr1-1-86 were separately compared with the reference, wild-type V5834, at the three time points (12SD, 16SD, 20SD) resulting in altogether six microarray hybridizations.

2005-11-23 | E-MEXP-491 | biostudies-arrayexpress

Transcription profiling of strains of Paxillus involutus that show different abilities in formation of ectomycorrhizal associations with birch (Betula pendula)

Project description:A microarray analysis was conducted to investigate transcriptional differences between strains of Paxillus involutus that show different abilities in formation of ectomycorrhizal associations with birch (Betula pendula). Our goal was to identify genes that showed differential regulation from comparing incompatible (not mycorrhiza forming) (Nau) and compatible (mycorrhiza forming) strains (ATCC200175 and Maj) of P. involutus, in association with birch. The entire design involved 11 slides (ME01-M11), 13 labelled extracts, and 3 biological replicates (Rep1-Rep3). The experiment was designed as a simple loop (all-pairwise comparisons) of all three strains including dye-swap, biological and technical replication. Additional information: In our pre-processing of data, 4 channels were excluded for further analyses due to overall poor quality and are listed below. Slide ME03, Cy5(635nm) (strain Nau, Rep2) Slide ME04, Cy5(635nm) (strain Nau, Rep2) Slide ME06, Cy5(635nm) (strain Maj, Rep2) Slide ME09, Cy5(635nm) (strain Nau, Rep2)

2004-10-05 | E-MEXP-179 | biostudies-arrayexpress

Response of peripheral blood mononuclear cells from patients with allergy to cat and silver birch wood derived antigenic peptide stimulation.

Project description:CD4 T cell responses are characterized based on a limited number of molecular markers selected from exisiting knowledge. The goal of the experiment was to assess antigenic-peptide specific T-cell responses in vitro without bias using microarrays. PBMCs were isolated from 2 donors with allergy. The cells were stimulated with antigenic peptides derived from silver birch wood and cat for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

2016-08-15 | E-GEOD-72373 | biostudies-arrayexpress

Comparative proteomics of common allergenic tree pollens of birch, alder and hazelComparative proteomics of common allergenic tree pollens of birch, alder and hazel

Project description:It is known that, in addition to known allergens, other proteins in pollen can aid the development of an immune response in allergenic individuals. The contribution of the “unknown” protein allergens becomes especially prominent in phylogenetically related species where, despite of high homology of the lead allergens, the degree of allergenic potential can greatly vary. The aim of this study was to identify other potentially allergenic proteins in pollen of three common and very related allergenic tree species: birch (Betula pendula), hazel (Corylus avellana) and alder (Alnus glutinosa). For that purpose, we carried out a comprehensive, comparative proteomic screening of the pollen from the three species. In order to maximize protein recovery and coverage, different protein extraction and isolation strategies during sample preparation were employed. As a result, we report 2500 - 3000 identified proteins per each of the pollen species. Identified proteins were further used for a number of annotation steps, providing insight into differential distribution of peptidases, peptidase inhibitors and other potential allergenic proteins across the three species. Moreover, we carried out functional enrichment analysis that, interestingly, corroborated high species similarity in spite of their relatively distinct protein profiles. We provide to our knowledge first insight into proteomes of three very important allergenic pollen types, which is particularly vital for pollen of hazel and alder where not even transcriptomics data is available. Datasets provided in this study can be readily used as protein databases, and as such serve as an excellent starting point for further allergenic studies.

2021-04-21 | PXD021133 | Pride

Gene expression analysis of nasal mucosa in birch pollen allergic and non-allergic individuals upon nasal provocation with birch pollen

Project description:Birch pollen is a significant cause of allergic rhinitis, yet the mechanisms of sensitization is to be understood completely. Here, we investigate the changes in gene expression of birch pollen allergic and non-allergic individuals that occur as a result of nasal provocation with birch pollen.

2024-12-17 | GSE261239 | GEO

Transcriptomic analysis of silver-resistant Saccharomyces cerevisiae mutant obtained by evolutionary engineering

Project description:Silver-resistant Saccharomyces cerevisiae mutant was obtained by evolutionary engineering method. Briefly, genetic diversity in reference strain, CEN.PK.113-7D, was increased by ethyl methane sulfonate (EMS)-mutagenesis. The mutant population was passaged several times in gradually increasing silver stress. Several mutant individuals were selected from the final population. Among selected mutant individuals, one of them was much more resistant to silver stress than the reference strain, called as 2E. Whole-genome transcriptomic analysis was performed to identify the silver resistance mechanisms in the silver-resistant mutant strain.

2020-01-09 | GSE143335 | GEO

Toxicogenomic responses of Caenorhabditis elegans exposed to sulfidized silver nanoparticles

Project description:We assessed the whole genome response of C. elegans exposed for 48 hours from L1 to the pristine silver nanomterials, artifically aged silver nanomatierls, and AgNO3. Single time point RNA extraction from a population of 2000-3000 nematodes exposed to the EC30 for reproduction.

2015-08-22 | E-GEOD-70509 | biostudies-arrayexpress

Betula pendula

Project description:Betula pendula var. pendula, Betula pendula var. carelica Raw sequence reads

| PRJNA1173919 | ENA

Betula pendula

Project description:Betula pendula Map

| PRJNA72331 | ENA