Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Investigation of millet genetic variants

ABSTRACT: An investigation into the genetic variation of millet cultivated germplasm

INSTRUMENT(S): Illumina HiSeq 4000

ORGANISM(S): Setaria Italica

SUBMITTER: Institute of Millet

PROVIDER: PRJEB45075 | EVA | 2021-05-22

REPOSITORIES: EVA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	millet_selected_snps.accessioned.vcf.gz	Vcf
	millet_selected_snps.accessioned.vcf.gz.csi	Vcf
	millet_selected_snps.accessioned.vcf.gz.tbi	Vcf
	millet_selected_snps.vcf.gz	Vcf
	millet_selected_snps.vcf.gz.csi	Vcf

Items per page:

1 - 5 of 6

Similar Datasets

Investigation of cattle genetic variants

Project description:An investigation into a sub set of cattle genetic variantion

| PRJEB75603 | ENA

Zea mays subsp. mays Transcriptome or Gene expression

Project description:Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a NAC gene (ZmNAC111) is significantly associated with natural variation in maize drought tolerance. For maize RNA-seq analysis, pooled tissues from three, eight-day-old maize seedlings were collected from transgenic and wild-type plants, prior to or after 2-hour dehydration, to conduct the RNA-seq analysis.

2015-03-29 | E-MTAB-4246 | biostudies-arrayexpress

Identification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations

Project description:In addition to the differences between populations in transcriptional and translational regulation of genes, alternative pre-mRNA splicing (AS) is also likely to play an important role in regulating gene expression and generating variation in mRNA and protein isoforms. Recently, the genetic contribution to transcript isoform variation has been reported in individuals of recent European descent. We report here results of an investigation of the differences in AS patterns between human populations. AS patterns in 176 HapMap lymphoblastoid cell lines derived from individuals of European and African ancestry were evaluated using the Affymetrix GeneChip Human Exon 1.0 ST Array. A variety of biological processes such as immune response and mRNA metabolic process were found to be enriched among the differentially spliced genes. The differentially spliced genes also include some involved in human diseases that have different prevalence or susceptibility between populations. The genetic contribution to the population differences in transcript isoform variation was then evaluated by a genome-wide association using the HapMap genotypic data on single nucleotide polymorphisms (SNPs). The results suggest that local and distant genetic variants account for a substantial fraction of the observed transcript isoform variation between human populations. Exon level expression on 176 HapMap cell lines.

2010-08-19 | E-GEOD-9703 | biostudies-arrayexpress

Identification of Common Genetic Variants that Account for Transcript Isoform Variation between Human Populations

2009-03-23 | GSE9703 | GEO

Transcriptomic and Genetic Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6

Project description:Low temperature is one of the major factors affecting rice germination, and low tempera-ture germination (LTG) is an important agronomic trait. Although genetic variation is abundant in rice germplasm resources, the molecular mechanism of LTG remains poorly understood. In this study, we first proved that weedy rice WR04-6 had significantly better low-temperature germination (LTG) ability at 10°C than the cultivated rice Qishanzhan (QSZ). RNA-seq was used to investigate the gene expression of WR04-6 and QSZ at 10, 12 and 14 days of seed germination at 10°C. The results of GO enrichment and KEGG en-richment revealed that the differentially expressed genes between WR04-6 and QSZ were mainly concentrated on the response to starch catabolic processes and the response to ab-scisic acid. This is consistent with the results of α-amylase activity, ABA and GA treat-ment. A recombinant inbred line (RIL) population derived from a cross between WR04-6 and QSZ and its high density SNP genetic map were used to detect quantitative trait loci (QTL) for low temperature germination rates at 10°C for 14 days. The results showed that two new QTLs were located on chromosome 3 and chromosome 12. Combined with the mapped QTLs and RNA-seq differential genes (DEGs), sixteen candidate genes potentially associated with LTG were identified. Validation of expression of the candidates by qRT-PCR were consistent with the RNA-seq data. These results will enable us to under-stand the genetic basis of LTG in weedy rice and provide new genetic resources for gener-ation of rice germplasm with LTG.

2023-03-01 | GSE222929 | GEO

Investigation into the Genetic Control of Micronutrient Metabolism

Project description:Investigation into the Genetic Control of Micronutrient Metabolism

| PRJNA258427 | ENA

Investigation of genetic compensation in tdp1-/- zebrafish embryos

Project description:Investigation of genetic compensation in tdp1-/- zebrafish embryos

| PRJNA626551 | ENA

Investigation of genetic dependencies in atypical teratoid rhabdoid tumors

Project description:Investigation of genetic dependencies in atypical teratoid rhabdoid tumors

| PRJNA963011 | ENA

Identification of genetic variants that affect histone modifications in human cells

Project description:Histone modifications are important markers of function and chromatin state, yet the DNA elements that direct them to specific locations in the genome are poorly understood. Here we use the genetic variation in Yoruba lymphoblastoid cell lines as a natural experiment to identify genetic differences that affect histone marks and to better understand their relationship with transcriptional regulation. Across the genome, we identified hundreds of quantitative trait loci that impact histone modification or RNA polymerase (PolII) occupancy. In many cases the same variant is associated with quantitative changes in multiple histone marks and PolII, as well as in DNaseI sensitivity and nucleosome positioning, indicating that these molecular phenotypes often share a single underlying genetic cause. Variants that impact chromatin at distal regulatory sites frequently also direct changes in chromatin and gene expression at associated promoters; while most of these distal regulators enhance promoter activity, some act as distal chromatin silencers. Finally, we find that polymorphisms in transcription factor binding sites are often causally responsible for variation in local histone modification. In summary, the class of variants identified here generate coordinated changes in chromatin both locally and sometimes at distant locations, frequently drive changes in gene expression, and likely play an important role in the genetics of complex traits. ChIP-seq of RNA Polymerase II and 4 histone modifications (H3K4me1, H3K4me3, H3K27ac, H3K27me3) in 10 unrelated Yoruba HapMap lymphoblastoid cell lines

2013-10-01 | E-GEOD-47991 | biostudies-arrayexpress

Pediatric Investigation of Genetic Factors Linked with Renal Progression (PediGFR)

Project description:Pediatric Investigation of Genetic Factors Linked with Renal Progression (PediGFR)

| PRJNA268993 | ENA