Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genomic resources for a historical collection of cultivated two-row European spring barley genotypes.

ABSTRACT: In this project we developed a data resource based on 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages with shallow whole genome shotgun sequencing to complement the RNA-sequencing data for variant calling.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Hordeum Vulgare

SUBMITTER: JHI

PROVIDER: PRJEB65875 | EVA | 2023-09-08

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	GeneSet_V2.accessioned.vcf.gz	Vcf
	GeneSet_V2.accessioned.vcf.gz.csi	Vcf
	GeneSet_V2.vcf.csi	Other
	GeneSet_V2.vcf.gz	Vcf
	MarkerSet_V2.accessioned.vcf.gz	Vcf

Items per page:

1 - 5 of 8

Similar Datasets

RNA-seq data from peduncle tissue of cultivated two-row European spring barley genotypes

Project description:In this project we developed a data resource based on a historical collection of 209 two-row European spring barley genotypes. The population is representative of pan-European breeding progress across the years from 1830 to 2014. The dataset comprises gene expression data generated by RNA-sequencing data of six different tissues across a range of developmental stages. This submission contains the peduncle tissue samples.

2023-08-21 | E-MTAB-13232 | biostudies-arrayexpress

RNA-seq data from inflorescence tissue of cultivated two-row European spring barley genotypes

2023-08-21 | E-MTAB-13233 | biostudies-arrayexpress

RNA-seq data from root tissue of cultivated two-row European spring barley genotypes

2023-08-21 | E-MTAB-13235 | biostudies-arrayexpress

RNA-seq data from crown tissue of cultivated two-row European spring barley genotypes

2023-08-21 | E-MTAB-13234 | biostudies-arrayexpress

RNA-seq data from grain tissue of cultivated two-row European spring barley genotypes

2023-08-21 | E-MTAB-13236 | biostudies-arrayexpress

RNA-seq data from spikelet tissues of cultivated two-row European spring barley genotypes.

2023-08-22 | E-MTAB-13231 | biostudies-arrayexpress

Evaluation of two methods for LS-MS/MS proteomic analysis of formalin fixed and paraffin embedded tissues

Project description:The proteomics of archival samples has advanced significantly during the last two decades, making possible the use of vast FFPE tissue archives in biomarker studies. However, due to the limited data regarding comparison of the performance of different protocols, there is currently no consensus on the most effective protocol for shotgun proteomic analysis of FFPE tissue. In-solution digestion method using Rapigest as detergent and FASP method, both reported to deliver superior results on FFPE tissues were compared using two label-free data-independent LC-MS/MS acquisition modes. Archival FFPE prostate tissues stored 7 years and mirroring fresh frozen samples were processed with both protocols in 3 technical replicates. Data were comparatively evaluated in terms of protein and peptide identifications in fresh frozen and FFPE samples, analysis of the fresh and FFPE tissues representative proteome (molecular weight distribution, distribution according to protein’s pI, cellular component analysis of proteins and quantitation accuracy) and technical reproducibility of the Rapigest and FASP protocols.

2021-01-15 | PXD021074 | Pride

Identification of the molecular basis of anti-cancer effect of Huaier.

Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None. Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes. For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..

| 2612481 | ecrin-mdr-crc

DIA-MS analysis of 21 breast cancer tissues

Project description:In recent years genomic and proteomic technologies have been employed in a combined effort to extrapolate key clinical and biological information of complex diseases such as cancer. Most integrative studies employ DNA and/or RNA sequencing technologies coupled to mass spectrometry-derived information to achieve deep information extraction levels, resulting in massive experimental efforts. In this context the employment of data independent acquisition (DIA) methods, which generally do not rely on fractionation, has seldom been tested. In this study, we evaluated the ability of DIA and data dependent acquisition (DDA) MS in determining key biological features of a set of 21 breast cancer tissues for whose RNA-sequencing data was also collected. We evaluated how proteomic data layers matched RNA analysis-derived genomic information, their degree of consensus, and their discrepancies.

2021-04-26 | PXD018830 | Pride

DIA-MS analysis of 24 breast cancer tissues

2021-04-26 | PXD021394 | Pride