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ABSTRACT:
PROVIDER: PRJEB76239 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Global genomic diversity of hexaploid oat
| PRJEB63645 | ENA
Project description:We profiled genome-wide gene expression changes in newly hybridized triploids (ABD), its genome-duplicated hexaploid (AABBDD), stable synthetic hexaploid (AABBDD) and T. turgidum (AABB) and Ae. tauschii (DD) parental lines of two independent crosses to reconstruct the events of allopolyploidization and genome stabilization.
2015-08-01 | GSE64883 | GEO
Project description:Gene expression levels of newly synthetic triploid wheat (ABD), its chromosome-doubled hexaploid (AABBDD), stable synthetic hexaploid (AABBDD), and their parents, Triticum turgidum (accession KU124, AABB) and Aegilops tauschii (accession KU2074, DD) were compared to understand genome-wide change of gene expressions during the course of amphidiploidization and genome stabilization. Stable synthetic hexaploid which were maintained through self-pollinations for 13 generations using the same combinations of the parents for production of synthetic common wheat.
2014-11-30 | GSE54398 | GEO
Project description:We describe a unique phenotype, blastulation failure, in three primary infertile males with oligoasthenoteratozoospermia (OAT) who underwent intracytoplasmic sperm injection (ICSI), resulting in multiple good-quality cleavage embryos that repeatedly failed to achieve blastulation or implantation. Single-cell analysis revealed that the arrested embryos had complex spermatozoa-derived chromosomal abnormalities, major embryonic genome activation failure, and overactivation of stress and apoptosis pathways at the transcriptional level. We further identified mutations in the meiosis-specific kinetochore factor MEIKIN gene in these males, causing OAT and chromosomal chaos in the spermatozoa. This study is the first to establish a connection between the genetic etiology of OAT and a novel embryo development arrest phenotype, indicating potenial risks of ICSI for OAT patients and providing a new explanation for recurrent implantation failure.
2024-06-30 | GSE234683 | GEO
Project description:Wheat is a cereal grain and one of the world’s major food crops. Recent advances in wheat genome sequencing are by now facilitating genomic and proteomic analyses of this crop. However, little is known about the protein levels of hexaploid versus tetraploid wheat cultivars, and knowledge on phosphorylated proteins still limited. Using our recently established (phospho)proteomic workflow, we performed a parallel analysis of the proteome and phosphoproteome on seedling leaves from two hexaploid wheat cultivars (Pavon 76 and USU-Apogee) and a tetraploid wheat (Senatore Cappelli). This revealed that a large portion of proteins and phosphosites can be quantified in all cultivars. Our shotgun proteomics data revealed a high similarity between hexaploid and tetraploid varieties with respect to protein abundance. However, we could identify a set of proteins that were differentially abundant between hexaploid and tetraploid cultivars. In addition, already at seedling stage, a small set of proteins were differential between the small (USU-Apogee) and larger hexaploid wheat cultivar (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.
2017-04-03 | PXD005437 | Pride
Project description:The complete assembly of vast and complex plant genomes, like the hexaploid wheat genome, remains challenging. Here, we present CS-IAAS, a comprehensive telomere-to-telomere (T2T) gap-free Triticum aestivum L. reference genome, encompassing 14.51 billion base pairs and featuring all 21 centromeres and 42 telomeres. Annotation revealed 90.8 Mb additional centromeric satellite arrays and 5,611 ribosomal DNA(rDNA) units. Genome-wide rearrangements, centromeric elements, TE expansion, and segmental duplications were deciphered during tetraploidization and hexaploidization, providing a comprehensive understanding of wheat subgenome evolution. Among them, TE insertions during hexaploidization greatly influenced gene expression balances, thus increasing the genome plasticity of transcriptional levels. Additionally, we generated 163,329 full-length cDNA sequences and proteomic data that helped annotate 141,035 high-confidence (HC) protein-coding genes. However, in such a hexaploidy genome, 20.05%, 33.43%, and 42.76% of gene transcript levels, alternative splicing events, and protein levels were detected unbalancing among subgenomes. The complete T2T reference genome (CS-IAAS), along with its transcriptome and proteome, represents a significant step in our understanding of wheat genome complexity, and provides insights for future wheat research and breeding.
2024-12-29 | PXD050500 | Pride
Project description:Purpose: The goal of this study was to analyse RNA-seq data to determine the effect of deletion of the RNA-binding protein HuD in transcriptiome-wide alternative splicing and polyadenylation in the neocortex of adult HuD KO vs. wild type littermates (controls) Methods: Cortical mRNA profiles of adult HuD KO (Elavl4 -/-) mice and Control mice were generated by RNA sequencing, in triplicate, using Illumina NovaSeq 6000 platform. The quality of raw RNA-sequencing reads was evaluated using FastQC software (version 0.11.5) and adapters were removed using the Cutadapt (version 1.15) and Trimmomatic (version 0.38) software. Alternative splicing was evaluated using rMATS software (version 4.0.2) and BAM files were converted to BedGraph before examining alternative polyadenylation using DaPars software (version 0.9.1) Methods (cont.): RNA-seq data was aligned to the M musculus genome (UCSC browser, mm10) using STAR (version 2.7.3a), and MultiQC (version 1.8) was used to perform a final quality check on STAR alignment files. If alignments were found to be the same read length and have >80% reads mapped to a unique location, the data was considered good quality and alternative splicing and polyadenylation analyses were performed. Sequence reads per sample were aligned to the mouse genome (build mm10). Results: HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2. In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of the proximal polyadenylation signal (PAS), resulting in shorter 3’ untranslated regions (3’ UTRs). Conclusions: HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.
2021-03-17 | GSE169023 | GEO
Project description:Oat beta glucan versus iso dietary fiber or placebo in MASLD: A multicenter, randomized, placebo-controlled dietary study
| PRJEB73985 | ENA
Project description:We profiled genome-wide gene expression levels in natural hexaploid. Chinese spring and three accessions were used.
2015-08-01 | GSE65262 | GEO