Ontology highlight
ABSTRACT:
PROVIDER: PRJNA913463 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs.
2016-07-05 | GSE83910 | GEO
Project description:DNA replication must be tightly controlled during each cell cycle to prevent unscheduled replication and ensure proper genome maintenance. The currently known controls that prevent re-replication act redundantly to inhibit pre-Replicative Complex (pre-RC) assembly outside of the G1 phase of the cell cycle. We have analyzed the effects of re-replication on the S. cerevisiae genome using a combination of Comparitive Genomic Hybridization (CGH) of re-replicating strains and Genome-Wide Location Analysis of pre-RC components. These data indicate which sites in the genome assemble pre-RCs under re-replication conditions, which sites undergo re-initiation and the extent of re-replication. Keywords: comparative genomic hybridization, ChIP-chip, re-replication, DNA replication, pre-RC
2006-03-20 | GSE4487 | GEO
Project description:In this study, we have characterized a putative chloroplast ribosome assembly factor. To elucidate transcriptional responses caused by decreased chloroplast function, we have measured the transcriptome of wild-type and knock-down seedlings.
2018-08-16 | E-MTAB-6866 | biostudies-arrayexpress
Project description:Chloroplast biogenesis represents a crucial step in seedling development, and is essential for the transition to autotrophic growth in plants. This light-controlled process relies on the transcription of nuclear and plastid genomes that drives the effective assembly and regulation of the photosynthetic machinery. Here we reveal a novel regulation level for this process by showing the involvement of chromatin remodelling in the coordination of nuclear and plastid gene expression for proper chloroplast biogenesis and function. The two Arabidopsis homologs of the yeast EPL1 proteins, core components of the NuA4 histone acetyl-transferase complex, are essential for the correct assembly and performance of chloroplasts. EPL1 proteins are necessary for the coordinated expression of nuclear genes encoding most of the components of chloroplast transcriptional machinery, specifically promoting H4K5Ac deposition in these loci. These data unveil a key participation of epigenetic regulatory mechanisms in the coordinated expression of the nuclear and plastid genomes.
2022-07-26 | GSE180614 | GEO
Project description:We found that thylakoid-anchored protein PBF8 is a key regulator for Photosystem I (PSI) biogenesis. To explore the role of PBF8 in regulating chloroplast gene expression, we performed the RNA-seq to compare the the transcript levels of chloroplast-encoded genes between wild type (Col-0) and pbf8 mutants. To this end, we isolated the total RNA form 12-day-old wild type and pbf8 seedlings grown on the MS medium under long-day conditions (14 h light, 10 h dark) at 22 ºC and with a light intensity of 80 µmol m-2 s-1. The rRNAs were deleted using the Ribo-Zero Kit (Epicentre). The resulting rRNA-depleted RNA was used for preparing the sequencing library with NEBNext Single Cell/Low input library Prep Kit. The libraries were pooled and sequenced on an Illumina Nova 6000 system with 150-bp pair-end reads. Finally, our results show that the transcript accumulation for chloroplast-encoded PSI subunit and assembly factor genes between the wild type (Col-0) and pbf8 samples, suggesting PBF8 may not affect the transcript levels of chloroplast-encoded PSI subunits and assembly factors in chloroplasts.
2024-01-24 | GSE239827 | GEO
Project description:The coordination of chloroplast and nuclear genome status are critical for plant cell function, but the mechanism remain largely unclear. In this study, we report that Arabidopsis thaliana CHLOROPLAST AND NUCLEUS DUAL-LOCALIZED PROTEIN 1 (CND1) maintains genome stability in both the chloroplast and the nucleus.
2022-12-13 | GSE220489 | GEO
Project description:Porcine 60K BeadChip genotyping arrays (Illumina) are increasingly being applied in pig genomics to validate SNPs identified by re-sequencing or assembly-versus-assembly method. Here we report that more than 98% SNPs identified from the porcine 60K BeadChip genotyping array (Illumina) were consistent with the SNPs identified from the assembly-based method. This result demonstrates that whole-genome de novo assembly is a reliable approach to deriving accurate maps of SNPs. To compare SNPs identified by genotyping arrays and de novo assembly method, we genotyped 10 pig breeds by porcine 60K BeadChip genotyping array (Illumina), including 1 berkshire pig, 1 hampshire pig, 1 landrace pig, 1 large white pig,1 piétrain pig, 1 bamei pig,1 jinhua pig, 1 meishan pig, 1 rongchang pig and 1 Tibetan wild boar.
2016-07-05 | E-GEOD-83910 | biostudies-arrayexpress
Project description:Duckweeds are a monophyletic group of rapidly reproducing aquatic monocots in the Lemnaceae family. Spirodela polyrhiza, the Greater Duckweed, has the largest body plan yet the smallest genome size in the family (1C = 150 Mb). Given their clonal, exponentially fast reproduction, a key question is whether genome structure is conserved across the species in the absence of meiotic recombination. We generated a highly contiguous, chromosome-scale assembly of Spirodela polyrhiza line Sp7498 using Oxford Nanopore plus Hi-C scaffolding (Sp7498_HiC) that is highly syntenic with a related line (Sp9509). Both the Sp7498_HiC and Sp9509 genome assemblies reveal large chromosomal misorientations in a recent PacBio assembly of Sp7498, highlighting the necessity of orthogonal long-range scaffolding techniques like Hi-C and BioNano optical mapping. Proteome analysis of Sp7498 verified the expression of nearly 2,250 proteins and revealed a high level of proteins involved in photosynthesis and carbohydrate metabolism among other functions. In addition, a strong increase in chloroplast proteins was observed that correlated to chloroplast density. This Sp7498_HiC genome was generated cheaply and quickly with a single Oxford Nanopore MinION flow cell and one Hi-C library in a classroom setting. Combining these data with a mass spectrometry-generated proteome, demonstrates that duckweed is a model for genomics- and proteomics-based education.
2022-10-26 | PXD017093 | Pride
Project description:<p>Genome-wide association studies (GWAS) identified thousands of genetic loci associated with complex plant traits, including many traits of agronomical importance. However, functional interpretation of GWAS results remains challenging because of large candidate regions due to linkage disequilibrium. High-throughput omics technologies, such as genomics, transcriptomics, proteomics, and metabolomics open new avenues for integrative systems biological analyses and help to nominate systems information supported (prime) candidate genes. In the present study, we capitalize on a diverse canola population with spring-type 477 lines which was previously analysed by high-throughput phenotyping (Knoch et al., 2020), and by RNA sequencing and metabolite profiling for multi-omics-based hybrid performance prediction (Knoch et al., 2021). We deepened the phenotypic data analysis, now providing 123 time-resolved image-based traits, to gain insight into the complex relations during early vegetative growth and re-analysed the transcriptome data based on the latest Darmor-bzh v10 genome assembly (Rousseau-Gueutin et al., 2020). Genome-wide association testing revealed 61,298 robust quantitative trait loci (QTL) including 187 metabolite-QTL, 56,814 expression-QTL, and 4,297 phenotypic QTL, many clustered in pronounced hotspots. Combining information about QTL colocalisation across omics layers and correlations between omics features allowed us to discover prime candidate genes for metabolic and vegetative growth variation. Prioritized candidate genes for early biomass accumulation include A06p05760.1_BnaDAR (PIAL1), A10p16280.1_BnaDAR, C07p48260.1_BnaDAR (PRL1), and C07p48510.1_BnaDAR (CLPR4). Moreover, we observed unequal effects of the Brassica A and C subgenomes on early biomass production.</p><p><br></p>
2023-11-20 | MTBLS8056 | MetaboLights
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc