Ontology highlight
ABSTRACT:
PROVIDER: PRJEB51985 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SAP.raw.vcf.csi | Raw | |||
| SAP.raw.vcf.gz | Vcf |
Items per page: 5 1 - 2 of 2 |
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Project description:Sorghum Association Panel Whole-Genome Sequencing Establishes Pivotal Resource for Dissecting Genomic Diversity
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Project description:Sorghum is a C4 cereal important not only as food, but also as forage and a bioenergy resource. Its resistance to harsh environments has made it an agriculturally important research subject. Recent accumulation of genomic and transcriptomic information has facilitated genetic studies. Yet genome-wide translational profiles in sorghum are still missing, although increasing evidence has demonstrated that translation is an important regulatory step, and the transcriptome does not necessarily reflect the profile of functional protein production in some organisms. Deep sequencing of ribosome-protected mRNA fragments (ribosome profiling, or Ribo-seq) has enabled genome-wide analysis of translation. In this study, we took advantage of Ribo-seq and identified actively translated reading frames throughout the genome. We detected translation of 7,304 main ORFs annotated in the sorghum reference genome version 3.1 and revealed a number of unannotated translational events. A comparison of the transcriptome and translatome between sorghums grown under normal and sulfur-deficient conditions revealed that gene expression is modulated independently at transcript levels and translation levels. Our study revealed the translational landscape of sorghum’s response to sulfur and provides datasets that could serve as a fundamental resource to extend research on sorghum, including translational studies.
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Project description:Identify genes in the epididymal adipose tissue whose expression is under genetic regulation in the hybrid mouse diversity panel. The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness. GWAS for expression of epididymal adipose tissue in inbred strains
2013-01-09 | E-GEOD-42890 | biostudies-arrayexpress
Project description:Identify genes in the heart whose expressions under genetic regulation in the hybrid mouse diversity panel. The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010. These data used to identify candidate genes at loci associated with atherosclerosis.
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Project description:Identify genes in the epididymal adipose tissue whose expression is under genetic regulation in the hybrid mouse diversity panel. The hybrid mouse diversity panel is comprised of classical inbred and recombinant inbred wild type mice. The RMA values of genes were used for genome wide association as described in Bennett et al Genome Research 2010. These data are used to identify candidate genes at loci associated with obesity and dietary responsiveness.
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Project description:Whole-genome sequencing of the Sorghum Association Panel
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Project description:To understand the full range of expression variation, alternative splicing, and the genetics of regulatory variation in humans, we have sequenced the genomes, exomes, and transcriptomes of 45 individuals in the Human Genome Diversity Panel (HGDP) from seven worldwide populations that span the geographic breadth of human migration history. We find few genes that are systematically differentially expressed among populations. Further, allelic expression analysis indicates that previously mapped common regulatory variants identified in eight HapMap3 populations have similar effects across HGDP populations, suggesting that the cellular effects of common variants are shared even across very diverse populations. In contrast, comparisons of alternative splicing across pairwise populations reveal highly significant differences, with ~20% of alternatively spliced exons varying significantly by population. Greater genomic differences are associated with significantly more splicing variability overall. Together, these results provide a resource and an estimate for the degree of sharing of gene expression, alternative splicing, and regulatory genetics across populations. Lymphoblastoid cell line mRNA profiles of 45 human samples from the Human Genome Diversity Panel sequenced on an Illumina HiSeq 2000, each sample library was sequenced in duplicate to produce a merged sample bam.
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