Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Exome capture of individuals from a Triticum aestivum cv Cadenza TILLING population

ABSTRACT: Exome capture of individuals from a Triticum aestivum cv Cadenza TILLING population

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Triticum Aestivum

SUBMITTER: TGAC

PROVIDER: PRJEB11524 | EVA | 2016-08-09

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	CAD_TILL_14042026_filtered_snpeff.accessioned.vcf.gz	Vcf
	CAD_TILL_14042026_filtered_snpeff.accessioned.vcf.gz.csi	Vcf
	CAD_TILL_14042026_filtered_snpeff.vcf.csi	Other
	CAD_TILL_14042026_filtered_snpeff.vcf.gz	Vcf

Items per page:

1 - 4 of 4

Similar Datasets

Exome capture of individuals from a Triticum aestivum cv Cadenza TILLING population

Project description:Exome capture of individuals from a Triticum aestivum cv Cadenza TILLING population

| PRJEB11524 | ENA

Triticum aestivum

Project description:Triticum aestivum L. exome capture sequence reads

| PRJNA662818 | ENA

Triticum aestivum

Project description:Exome Capture raw sequence reads of Triticum aestivum for association Mapping of BYDV and SBWMV and FHB

| PRJNA1460287 | ENA

Cross-platform comparison of gene expression-based cancer molecular subtyping reveals discrepancies with exome capture methods

Project description:Gene expression profiling assays in precision oncology is increasing with uncertain validity across platforms. In this study, we examined the application of PurIST, a molecular subtyping algorithm for pancreatic ductal adenocarcinoma (PDAC), across different platforms. We compared PurIST calls between matched samples processed by whole transcriptome and commercial exome capture RNA-seq. In parallel, we compared subtypes between matched samples processed by NanoString and whole transcriptome RNA-seq from the PANCREAS trial (NCT04683315). Between whole transcriptome and exome capture, subtype agreement was 81% with significant increase in basal-like subtype with exome capture. Differences in overall survival in patients with basal-like tumors compared to classical tumors did not reach statistical significance using exome capture (log-rank P = 0.061), whereas with whole transcriptome it was significantly shorter (log-rank P < 0.0001). Subtype agreement between whole transcriptome RNA-seq and NanoString was higher at 95%. PurIST results should be interpreted with caution when using exome capture method.

2025-12-15 | GSE313117 | GEO

Triticum aestivum cultivar:Hahn

Project description:Triticum aestivum L. exome capture sequence reads. Cultivar: Hahn

| PRJNA663626 | ENA

Mapping the Triticum aestivum proteome

Project description:Wheat is the staple food of over 35% of the world’s population, accounts for 20% of all human calories, and its yield and quality improvement is a focus in the effort to meet new demands from population growth and changing diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. With the aim of creating a resource complementary to current genome sequencing and assembly projects and to aid researchers in the specific analysis and measurement of wheat proteins of interest, we present a large scale, publicly accessible database of identified peptides and proteins derived from the proteome mapping of Triticum aestivum. This current dataset consists of twenty four organ and developmental samples in an online interactive resource allowing the selection, comparison and retrieval of proteomic data with rich biochemical annotation derived from multiple sources. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified alongside hierarchical assessment of protein functional classes and their presence in different tissues. The impact of wheat’s polyploid genome on proteome analysis and the effect on defining gene specific and protein family relationships is accounted for in the organisation of the data. The dataset will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function.

2016-11-17 | PXD004720 | Pride

Whole-exome sequencing (WES) of single glands from opposite side of two colorectal tumors and WES of colorectal cancer xenografts derived from single cell culture to study tumor growth dynamics

Project description:Single Gland Whole-exome sequencing: building on our prior description of multi-region WES of colorectal tumors and targeted single gland sequencing (E-MTAB-2247), we performed WES of multiple single glands from different sides (right: A and left: B) of two tumors in this study (tumor O and U) on the illumina platform using the Agilent SureSelect 2.0 or illumina Nextera Rapid Capture Exome kit (SureSelect or NRCE, as indicated in the naming of fastq files). Colorectal Cancer Xenograft Whole-exome sequencing: The HCT116 and LoVo Mismatch-Repair-deficient colorectal adenocarcinoma cell lines were obtained from the ATCC and cultured under standard conditions. For both cell lines, a single âfoundingâ cell was cloned and expanded in vitro to ~6M cells. Two aliquots of ~1M cells were subcutaneously injected into opposite flanks (right and left) of a nude mouse and tumors allowed to reach a size of ~1B cells (1cm3) before the animal was sacrificed. Tumor tissue was collected separately from the right and left lesions and DNA was extracted for WES using the illumina TruSeq Exome kit or Nextera Rapid Capture Exome expanded Kits (Truseq or NRCEe), as was DNA from the first passage population (a polyclonal tissue culture for HCT116 and a polyclonal xenograft sample for LoVo), which were employed as a control to study mutation accumulation in culture and post xenotransplantation.

2017-05-01 | E-MTAB-5547 | biostudies-arrayexpress

Triticum aestivum

Project description:Triticum aestivum Exome

| PRJNA550304 | ENA

Triticum aestivum

Project description:Triticum aestivum probe capture sequences

| PRJNA349252 | ENA

Exome capture of pooled population samples of Pinus cembra (Swiss stone pine)

Project description:Exome capture of pooled population samples of Pinus cembra (Swiss stone pine)

| PRJEB41735 | ENA