Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Genotyping of Saccharum spp. association panel

PROVIDER: PRJNA702641 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13741144.fastq.gz	Fastqsanger.gz
	SRR13741145.fastq.gz	Fastqsanger.gz
	SRR13741146.fastq.gz	Fastqsanger.gz
	SRR13741147.fastq.gz	Fastqsanger.gz
	SRR13741148.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Project description:TCAP Spring wheat association mapping panel with Genotyping-by-Sequencing

| PRJNA641969 | ENA

rye_gbs_diversity_panel

Project description:Genotyping-by-sequencing data of a rye (Secale spp.) diversity panel

| PRJEB50548 | ENA

Project description:Cyclospora genotyping expanded panel

| PRJNA1130490 | ENA

Global analysis of the sugarcane microtranscriptome reveals a unique composition of small RNAs associated with axillary bud outgrowth

Project description:Axillary bud outgrowth determines plant shoot architecture and is under control of endogenous hormones and a fine-tuned gene expression network. Some genes associated with shoot development are known targets of small RNAs (sRNAs). Although it is well known that sRNAs act broadly in plant development, our understanding about their roles in vegetative bud outgrowth remains limited. Moreover, the expression profiles of microRNAs (miRNAs) and their targets in axillary buds are unknown. In this study, we employed next-generation sequencing, gene expression analysis and metabolite profiling to identify sRNAs and quantify distinct hormones, respectively, in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.). Differential accumulation of abscisic acid (ABA), gibberellins (GA), and cytokinins indicates a dynamic balance of these hormones during sugarcane bud outgrowth. A number of repeat-associated siRNAs generated from distinct transposable elements and genes were highly expressed in both inactive and developing buds. RT-qPCR results revealed that specific miRNAs were differentially expressed in developing buds and some correlate negatively with the expression of their targets. Expression patterns of miR159 and its experimentally confirmed target GAMYB suggest they play roles in regulating ABA and GA-signaling pathways during bud outgrowth. Our work reveals, for the first time, differences in composition and expression profiles of small RNAs and targets between inactive and developing buds that, together with the endogenous balance of specific hormones, may be important to regulate axillary bud outgrowth in plants. Examination of small RNA populations in vegetative axillary buds of the tropical biofuel crop sugarcane (Saccharum spp.)

2012-12-31 | E-GEOD-38894 | biostudies-arrayexpress

Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays

Project description:Low-pass sequencing (sequencing a genome to an average depth less than 1× coverage) combined with genotype imputation has been proposed as an alternative to genotyping arrays for trait mapping and calculation of polygenic scores. To empirically assess the relative performance of these technologies for different applications, we performed low-pass sequencing (targeting coverage levels of 0.5× and 1×) and array genotyping (using the Illumina Global Screening Array (GSA)) on 120 DNA samples derived from African and European-ancestry individuals that are part of the 1000 Genomes Project. We then imputed both the sequencing data and the genotyping array data to the 1000 Genomes Phase 3 haplotype reference panel using a leave- one-out design. We evaluated overall imputation accuracy from these different assays as well as overall power for GWAS from imputed data, and computed polygenic risk scores for coronary artery disease and breast cancer using previously derived weights. We conclude that low-pass sequencing plus imputation, in addition to providing a substantial increase in statistical power for genome wide association studies, provides increased accuracy for polygenic risk prediction at effective coverages of ∼ 0.5× and higher compared to the Illumina GSA.

2021-01-31 | GSE165845 | GEO

Standing at the gateway to Europe - the genetic structure of Western Balkan populations based on autosomal and haploid markers

Project description:Here we present genome-wide high-coverage genotyping data on a panel of 75 human samples from Western Balkan region, Europe, that are used in addition to public data in studing the genetic variation of Southern Europe that was sequenced to the avwerage depth of 1X.

2014-08-22 | GSE59032 | GEO

SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds

Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.

2013-05-09 | GSE46733 | GEO

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Project description:Here we present genome-wide high-coverage genotyping data on a panel of 85 human samples from Eurasia that are used in addition to public data in studing the genomic context of a 24 kya old DNA sample from Southern Siberia that was sequenced to the avwerage depth of 1X.

2013-11-18 | GSE50727 | GEO

ACTINOBACTERIA ASSOCIATED TO Anthurium spp. AS A SOURCE OF ACTIVE METABOLITES AGAINST BOVINE MASTITIS-CAUSING BACTERIA

Project description:Mgf files of the analysis of 66 extracts of 22 strains of Streptomyces spp. actinobacteria isolated in association to Anthurium spp. in brazilian oceanic islands, plus culture media blanks.

2022-04-19 | MSV000089281 | MassIVE

Project description:Sugarcane (Saccharum spp. hybrids) mitochondrial genomes

| PRJNA613602 | ENA