Del/Ros1 Tomato Genome Resequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34166 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Microarray analysis was used to compare the gene expression profiles of red and purple sectors of VIGS (Virus-induced gene silencing)-treated Del/Ros1 fruit in the MoneyMaker background. Fruit were silenced at the mature green stage and harvested at differing number of days after breaker.
2013-05-06 | GSE46341 | GEO
Project description:Microarray analysis was used to compare the gene expression profiles of red and purple sectors of VIGS (Virus-induced gene silencing)-treated Del/Ros1 fruit in the MoneyMaker background. Fruit were silenced at the mature green stage and harvested at differing number of days after breaker. Custom two-colour microarray (TOM2); where one channel was employed as a common reference.
2013-05-06 | E-GEOD-46341 | biostudies-arrayexpress
Project description:Transgenic plants carrying an estradiol-inducible ROS1-YFP construct (XVE:ROS1-YFP) were subjected to long-read sequencing (Oxford Nanopore Technologies) to assess the global impacts of ROS1 activity on the methylome of Arabidopsis thaliana (ecotype Col-0).
2022-11-07 | GSE211295 | GEO
Project description:To survey transcriptome changes by the mutations of a DNA demethylase ROS1 responding to a phytohormone abscisic acid, we performed the Next-gen sequencing (NGS) associated RNA-seq analysis. Two ROS1 knockout lines (ros1-3, ros1-4; Penterman et al. 2007 [PMID: 17409185]) with the wild-type Col line (wt) were subjected. Three samples (ros1-3, ros1-4 and wt), biological triplicates, ABA or mock treatment, using Illumina HiSeq 2500 system
2016-01-15 | E-GEOD-65016 | biostudies-arrayexpress
Project description:To survey transcriptome changes by the mutations of a DNA demethylase ROS1 responding to a phytohormone abscisic acid, we performed the Next-gen sequencing (NGS) associated RNA-seq analysis. Two ROS1 knockout lines (ros1-3, ros1-4; Penterman et al. 2007 [PMID: 17409185]) with the wild-type Col line (wt) were subjected.
2016-01-15 | GSE65016 | GEO
Project description:Arabidopsis ROS1 is the first genetically characterized DNA demethylase in eukaryotes. Dysfunction of ROS1 leads to increase in DNA methylation level at thousands of genomic loci. However, the features of ROS1 targets are not well understood. In this study, we identified and characterized ROS1 target loci in Arabidopsis Col-0 and C24 ecotypes. Most ROS1 targets are transposable elements (TEs) and intergenic regions. Compared to other TEs, ROS1-targeted TEs are closer to protein coding genes, suggesting a role for ROS1 in preventing the spreading of DNA methylation from highly methylated TEs to nearby genes. Interestingly, we found that unlike general TEs, ROS1 targets are associated with an enrichment of H3K18ac and H3K27me3, and depletion of H3K27me and H3K9me2. We investigated the antagonism between ROS1 and RNA-directed DNA methylation (RdDM) by identifying and characterizing thousands of genomic regions regulated by both ROS1 and RdDM. Unexpectedly, we uncovered thousands of previously unidentified RdDM targets by analyzing the DNA methylome of ros1/nrpd1 double mutant plants. In addition, we show that ROS1 also antagonizes RdDM-independent DNA methylation at more than a thousand genomic loci. Our results provide significant insights into the genome-wide effects of both ROS1-mediated active DNA demethylation and RNA-directed DNA methylation as well as their interaction in plants. Using small RNA-Seq(sRNA-Seq) to get small RNA profiling of WT, ros1-4, nrpd1 single mutants and ros1-4/nrpd1doubble mutant
2016-11-01 | GSE83800 | GEO
Project description:Aberrant DNA methylation is a hallmark of cancer but mechanisms contributing to the abnormality remain elusive. Here, we report that most of lung cancer cell lines tested expressed predominantly ∆DNMT3B-del whereas normal bronchial epithelial cells expressed equal quantities of ∆DNMT3B and ∆DNMT3B-del. We demonstrate biological impacts of ∆DNMT3B4-del, a ∆DNMT3B-del isoform, in a transgenic mouse model. Expression of ∆DNMT3B4-del in the mouse lungs resulted in an increased global DNA hypomethylation, focal DNA hypermethylation, epithelial hyperplastia and tumor formation when challenged with a tobacco carcinogen. In patients with non-small cell lung cancer, 83% of the primary tumors expressed predominantly ∆DNMT3B-del. Our results demonstrate ∆DNMT3B4-del as a critical factor in developing aberrant DNA methylation during lung tumorigenesis.
2017-02-09 | GSE68922 | GEO
Project description:Polyamines are aliphatic polycations that have emerged as important determinants of cell growth and viability in rapidly proliferating cells, including in the pathogenic protozoan parasite Leishmania donovani. In L. donovani, the polyamine spermidine is synthesized by the successive conversion of ornithine into putrescine (catalyzed by ornithine decarboxylase or ODC) and putrescine into spermidine (catalyzed by spermidine synthase or SPDSYN). Deletion of either ODC (del-odc) or SPDSYN (del-spdsyn) from the L. donovani genome renders these parasites auxotrophic for polyamines and these mutants are impaired in their ability to survive both in culture and within the mammalian host without the addition of exogenous polyamine supplementation. Significantly, del-odc parasites immediately cease proliferation after putrescine is removed from the culture media and perish within two weeks, while spermidine starved del-spdsyn mutants, which retain intracellular putrescine pools, show a slow-growth phenotype, and persist for several weeks in culture. To elucidate the key differences within the proteome of putrescine-starved del-odc cells and spermidine-starved del-spdsyn parasites, a shotgun quantitative proteomics approach was undertaken using TMT labeling and LC-MS/MS analysis. Briefly, three biological replicates each for mid-log phase del-odc and del-spdsyn promastigotes grown in the presence of exogenous putrescine (for del-odc) or spermidine (for del-spdsyn) supplementation were washed to remove the exogenous polyamine supplementation and incubated in polyamine-free media. At 24 and 48 h, cells from each biological replicate were isolated and prepared for tandem mass tag (TMT) labeling and downstream LC-MS/MS analyses. Peptides were identified using a database generated from the reference genome of L. donovani BPK282A1 strain. Changes in relative protein abundance for the polyamine-starved del-odc and del-spdsyn cell lines at 24 and 48 h were calculated by comparing aggregate total reporter ion intensities for each protein to that of the corresponding polyamine-supplemented 0-h timepoint.
2022-08-29 | PXD036349 | Pride
Project description:Using MethylC-Seq to provide single-base resolution of DNA methylation status in ros1-13 mutant Whole genome methylation maps of ros1-13 (with 35S-SUC2 transgene) was generated using BS-seq
2015-02-05 | E-GEOD-58790 | biostudies-arrayexpress
Project description:Using whole genome bisulfite sequencing to provide single-base resulution of DNA methylation status in rdm16ros1, ros1, nrpd1ros1 mutants and examine the effect of RDM16 on DNA methylation 4 samples examined: C24 wild type with RD29A-LUC transgene, rdm16ros1 double mutant, ros1 mutant, nrpd1ros1 mutant (all in C24 background with RD29A-LUC transgene)
2013-09-27 | E-GEOD-44417 | biostudies-arrayexpress