Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Chenopodium ucrainicum RADseq

PROVIDER: PRJNA950315 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR24015400_1.fastq.gz	Fastqsanger.gz
	SRR24015400_2.fastq.gz	Fastqsanger.gz
	SRR24015401_1.fastq.gz	Fastqsanger.gz
	SRR24015401_2.fastq.gz	Fastqsanger.gz
	SRR24015402_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 164

Similar Datasets

De novo characterization of foliar transcriptome in Chenopodium amaranticolor and analysis of the differentially expressed genes during the stage of hypersensative response induced by distinct plant viruses

Project description:The hypersensitive response (HR) system of Chenopodium spp. confers broad-spectrum virus resistance. However, scant knowledge exists at the genomic level for Chenopodium, thus impeding the advanced molecular research of this attractive feature. Hence we took advantage of RNA-seq to survey the foliar transcriptome of C. amaranticolor, one Chenopodium species being widely used as laboratory indicator for pathogenic viruses, in order to facilitate the characterization of the HR-type of virus resistance. In a single run, we obtained 39,868,984 reads with 3,588,208,560 bp, which were assembled into 112,453 unigenes (3,848 clusters and 108,605 singletons). BlastX search against the NCBI NR database identified 62,482 sequences with a cut-off E-value above 10-5. Assembled sequences were annotated with gene descriptions, GO, COG and KEGG terms. A dataset containing 738 resistance gene analogs and sequences represent 6 key signaling proteins within the R proteins-directed signaling pathway was generated. Additionally, using RNA-Seq digital gene expression analysis, we investigated the gene expression profiles over the stage of HR induced by Tobacco mosaic virus and Cucumber mosaic virus in C. amaranticolor leaves, and identified numerous candidate genes specifically or commonly regulated by these two distinct viruses at early and late stages of the HR. Specifically, the dynamic changes of the differently expressed genes enriched in the pathway of plant-pathogen interaction were analyzed. To our knowledge, this is the first study to elucidate the genetic makeup of Chenopodium spp., providing a starting-point for future functional genomics studies on Chenopodium.

2013-02-20 | GSE38451 | GEO

RADseq for tumour mutation burden estimation and mutation signature analysis.

Project description:The utility of RADseq in an experimental setting is also demonstrated, based on our chasacterisation of an APOBEC mutation signature in an APOBEC3A transfected mouse cell line. 0D5 cells, derived from SSM3 cells, were co-transfected with a mixture containing pcDNA3.1 vectors expressing either APOBEC3A or APOBEC3B (kindly donated by Vincent Caval), pcDNA3.1 construct expressing deaminase null APOBEC3A linked to a uracil deglycosylase construct and a plasmid encoding mutant GFP and WT mCherry that is a reporter for APOBEC mutagenesis. Cells were grown, and gDNA extracted, prior to preparation of RADseq libraries using a PstI- MspI double-digest. Libraries underwent a Pippin Prep to select fragments in the size range of 220-520 bp (genomic sequence plus 148 bp of adapters). Single-end sequencing (1x101bp) was performed on an Illumina NovaSeq6000 utilizing v1.5 chemistry. Reads were aligned to mm10 using bwa mem and variants called using the GATK4 pipeline.

2023-06-30 | GSE234146 | GEO

2013-02-20 | E-GEOD-38451 | biostudies-arrayexpress

Expression profiles of ABA treated bladder and leaf samples of Chenopodium quinoa

Project description:In this project, leaves and EBCs of the halophyte plant Chenopodium quinoa were treated with ABA. The effect of the ABA treatment was analyzed by comparing to non-treated leaves and EBCs.

2022-05-10 | E-MTAB-10419 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Chenopodium quinoa Transcriptomes

Project description:We generated 70.9 Gb of high-quality sequencing data (~7.88 Gb per sample) and catalogued the expression profiles of 54，238 annotated Chenopodium quinoa genes in each sample. These genes have known or potential roles in the roots, stems, and leaves of quinoa. Therefore, we are appealing candidates for further investigation of the gene expression and associated regulatory mechanisms.

2022-03-03 | GSE156523 | GEO

RADseq

Project description:RADseq

| PRJNA575770 | ENA

RADseq

Project description:RADseq

| PRJNA575772 | ENA

Chenopodium-quinoa-flower

Project description:Chemotyping dataset of n-butanol peptide extract of Chenopodium quinoa flower

2018-06-29 | MSV000082525 | MassIVE

Systematic Discovery of Deeply Conserved Plant Protein Complexes, Quinoa

Project description:The associated files are mass spec data from mixed-bed ion exchange chromatogrphy fractions. Starting extract was 14,000 x g clarified supernatant from extraction of liquid nitrogen powdered Chenopodium quinoa seeds. Extraction buffer was 20 mM HEPES pH 7.6, 130 mM K-acetate, 5 mM Mg-acetate, 0.1 mM EDTA, 10% glycerol, 1 mM DTT, phosphatase inhibitors, and Plant specific protease inhibitors.

2019-10-28 | PXD013080 | Pride

Project description:Chenopodium ficifolium sequencing

| PRJNA678370 | ENA