Ontology highlight
ABSTRACT:
PROVIDER: PRJNA832069 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:DNA methylation and histone H3 lysine 9 dimethylation (H3K9me2) are important epigenetic repression marks for silencing transposons in heterochromatin and regulating gene expression in plant development. However, the mechanistic relationship to other repressive marks, such as histone H3 lysine 27 trimethylation (H3K27me3), is unclear. OsFIE1 (Fertilization Independent Endosperm 1) encodes an Esc-like core component of the Polycomb repressive complex 2 (PRC2), which is involved in H3K27me3-mediated gene repression. Here, we identify a gain-of-function epi-allele (Epi-df) of rice OsFIE1; this allele exhibits a dwarf stature and various floral defects that are inherited in a dominant fashion. We found that Epi-df has no changes in its nucleotide sequence, but is hypo-methylated in the promoter and the 5' region of OsFIE1 and has reduced H3K9me2 and increased H3K4me3. In Epi-df, OsFIE1 was ectopically expressed and its imprinting status was disrupted. OsFIE1 interacted with rice E(z) homologs, consistent with its role in H3K27me3 repression. Ectopic expression of OsFIE1 in Epi-df resulted in alteration of H3K27me3 levels in hundreds of genes. Therefore, this work identifies a novel epi-allele involved in H3K27me3-mediated gene repression, that itself is highly regulated by histone H3K9me2, thereby shedding light on the link between two important epigenetic marks regulating rice development. We report the application of ChIP-Seq technology for high-throughput profiling of histone modifications in WT (wild type) and Epi-df (mutant). We demonstrate that the H3K27me3 status is perturbed at target genes and leads to mis-regulated expression in Epi-df.
2013-12-04 | E-GEOD-40674 | biostudies-arrayexpress
Project description:Copy-number variation (CNV) genotyping was run on 450 HapMap samples using a custom targeted array. The array contained 105 000 oligos targeted to about 10 000 CNVs.
2009-10-07 | E-MTAB-142 | biostudies-arrayexpress
Project description:Targeted genotyping-based identification of donor- and recipient-derived cells to resolve the origin of myelodysplastic syndrome (MDS) following allogeneic stem cell transplantation in the context of aplastic anemia (AA).
2024-12-06 | GSE228278 | GEO
Project description:we examined the glycoproteomics of N-glycosylation in untreated LNCaP (NC), ST-EPI, LT-EPI, ST-ENZ, and LT-ENZ groups using Tandem Mass Tag (TMT) labels by nanoscale liquid chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS).LNCaP-NC, SP-EPI, SP-ENZ, LP-EPI, and LP-ENZ cells each with two biological replicates were used for glycoproteomics analysis.
2022-08-12 | PXD030036 | Pride
Project description:Current approaches to track stem cell clones through differentiation require genetic engineering or rely on sparse somatic DNA variants. Here, we show that targeted single-cell measurements of DNA methylation at single-CpG resolution deliver joint information about cellular differentiation state and clonal identities. We develop EPI-clone, a method for transgene-free lineage tracing based on microfluidic, targeted single-cell DNA methylation analysis. Applied to mouse and human hematopoiesis, we captured hundreds of clonal differentiation trajectories across tens of individuals and almost 400,000 single-cells. Using ground-truth genetic barcodes, we demonstrate that EPI-clone accurately identifies clonal lineages throughout hematopoietic differentiation while at the same time providing cell state resolution similar to transcriptomic data. Applied to unperturbed hematopoiesis in murine ageing, we demonstrate that myeloid bias and low output of old HSCs are restricted to a small number of expanded developmental clones, while many functionally young-like clones persist in old age. In human ageing, we demonstrate that clones carrying CHIP mutations are part of a spectrum of age-related expansions of low-output clones. EPI-clone is compatible with the multiplexed readout of surface protein, somatic variants and RNA from the same single cell. Taken together, EPI-clone enables accurate and transgene-free single-cell lineage tracing on hematopoietic cell state landscapes at scale.
2024-12-31 | GSE282971 | GEO
Project description:We performed genotyping of Neuroblastoma Primary tumors using Illumina HumanHap 550 - v1,v3,v3duo and 610 Quad genotyping beadchips.
2011-09-15 | GSE19385 | GEO
Project description:Cyclospora cayetanensis genotyping using targeted amplicon sequencing
| PRJNA952552 | ENA