Similar Datasets
Project description:Origin Recognition Complex Associated (ORCA) associates with repressive chromatin environments. We carried out H3K9me3 ChIP-seq to determine the affect of ORCA's loss on this repressive mark. Towards this end, we cultured U2OS osteosarcoma cells, performed control and ORCA knockdowns using siRNAs and then carried out H3K9me3 ChIP-seq to determine the regions in the genome which get affected upon ORCA knockdown. Examination of the levels of H3K9me3 in control and ORCA knockdown cells
2015-04-28 | E-GEOD-68129 | biostudies-arrayexpress
Project description:ORCA is an ORC associated protein that plays important roles in replication initiation as well as heterochromatin organization. We carried out ORCA ChIP-seq in U2OS cells synchronized at different stage of G1 phase to determine its genome wide localization. To understand the genomic features of ORCA binding regions, we also carried out Methylated DNA IP (MeDIP) followed by deep sequencing in U2OS cells to determine the genome wide localizatoin of methyl-CpG sites in U2OS cells and how ORCA bidning regions co-localize with this important repressive mark.
2016-12-09 | GSE81165 | GEO
Project description:Origin Recognition Complex Associated (ORCA) associates with repressive chromatin environments. We carried out H3K9me3 ChIP-seq to determine the affect of ORCA's loss on this repressive mark. Towards this end, we cultured U2OS osteosarcoma cells, performed control and ORCA knockdowns using siRNAs and then carried out H3K9me3 ChIP-seq to determine the regions in the genome which get affected upon ORCA knockdown.
2015-04-28 | GSE68129 | GEO
Project description:Twenty-four patients were randomized to receive Orca-T alone (n=12) or Orca-T plus single-agent GVHD prophylaxis (n=12) to determine if Orca-T alone was non-inferior in preventing acute GVHD.
2024-03-06 | GSE230788 | GEO
Project description:ICGC PCAWG Dataset for WGS BAM aligned using BWA MEM. Project: ORCA-IN.
| EGAD00001002120 | EGA
Project description:Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for hematologic malignancies. The primary non-relapse complication after allo-HSCT is graft-versus-host disease (GVHD). The use of T regulatory (Treg) cells to prevent GVHD has emerged as a promising allogeneic T cell immunotherapy in the form of Orca-T. However, the precise differences in immune states which may influence clinical outcomes after Orca-T compared with unmanipulated peripheral blood stem cell (PBSC) grafts remain unexplored. Using peripheral blood specimens longitudinally collected between 3 weeks and one year after leukemia treatment, we examined single-nucleus ATAC-seq and whole transcriptome sequencing (scRNA-seq) analysis of PBMC from 4 patients receiving either Orca-T or unmanipulated PBSC grafts and 2 mobilized donors.
2026-05-27 | GSE312099 | GEO
Project description:Polycomb bodies, also called Polycomb group (PcG) protein complexes, are implicated in gene regulation, especially during development, differentiation, and during the maintenance of tissue-specific functions in multicellular organisms. Predominantly, in transformed cells, PcG bodies form distinct nuclear foci, within which PcG-bound DNA is localized. These structures likely represent misregulated gene expression due to the loss of normal regulatory mechanisms, yet the molecular function of these bodies in cellular homeostasis remains unknown. Using TSA-Seq (Tyramide signal amplification), we provide the first-of-a-kind comprehensive view of the genomic regions, including specific centromeric and telomeric sites that are in proximity to the PcG bodies. Further, these regions are enriched for the repressive histone marks, H3K27me3, H3K9me3 and depleted for active marks, H3K4me3 consistent with a lack of accessible chromatin. We find high density of replication origins around PcG bodies, consistent with the replication factor, ORCA/LRWD1 localizing at these sites. ORCA interacts with the PRC complex, stabilizes the H3K27 methyltransferase, and facilitates the deposition of this histone mark at specific chromatin sites. Loss of ORCA impacts the chromatin organization around the PcG bodies, leading to decompaction of the repeat regions, and enhanced initiation from replication origins. Our results indicate that ORCA interacts with the PcG complex-bound chromatin and maintains a repressed heterochromatin environment to control the timing of replication origin firing.
2026-06-15 | GSE314620 | GEO
Project description:Polycomb bodies, also called Polycomb group (PcG) protein complexes, are implicated in gene regulation, especially during development, differentiation, and during the maintenance of tissue-specific functions in multicellular organisms. Predominantly, in transformed cells, PcG bodies form distinct nuclear foci, within which PcG-bound DNA is localized. These structures likely represent misregulated gene expression due to the loss of normal regulatory mechanisms, yet the molecular function of these bodies in cellular homeostasis remains unknown. Using TSA-Seq (Tyramide signal amplification), we provide the first-of-a-kind comprehensive view of the genomic regions, including specific centromeric and telomeric sites that are in proximity to the PcG bodies. Further, these regions are enriched for the repressive histone marks, H3K27me3, H3K9me3 and depleted for active marks, H3K4me3 consistent with a lack of accessible chromatin. We find high density of replication origins around PcG bodies, consistent with the replication factor, ORCA/LRWD1 localizing at these sites. ORCA interacts with the PRC complex, stabilizes the H3K27 methyltransferase, and facilitates the deposition of this histone mark at specific chromatin sites. Loss of ORCA impacts the chromatin organization around the PcG bodies, leading to decompaction of the repeat regions, and enhanced initiation from replication origins. Our results indicate that ORCA interacts with the PcG complex-bound chromatin and maintains a repressed heterochromatin environment to control the timing of replication origin firing.
2026-06-15 | GSE291918 | GEO
Project description:Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for hematologic malignancies. The primary non-relapse complication after allo-HSCT is graft-versus-host disease (GVHD). The use of T regulatory (Treg) cells to prevent GVHD has emerged as a promising allogeneic T cell immunotherapy in the form of Orca-T. However, the precise differences in immune states which may influence clinical outcomes after Orca-T compared with unmanipulated peripheral blood stem cell (PBSC) grafts remain unexplored. Using peripheral blood specimens longitudinally collected between 3 weeks and one year after leukemia treatment, we examined single-cell mRNA sequencing (scRNA-seq) analysis of 16 HLA-matched patients receiving either Orca-T or unmanipulated PBSC grafts.
2026-03-01 | GSE290864 | GEO
Project description:Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a curative therapy for hematologic malignancies. The primary non-relapse complication after allo-HSCT is graft-versus-host disease (GVHD). The use of T regulatory (Treg) cells to prevent GVHD has emerged as a promising allogeneic T cell immunotherapy in the form of Orca-T. However, the precise differences in immune states which may influence clinical outcomes after Orca-T compared with unmanipulated peripheral blood stem cell (PBSC) grafts remain unexplored. Using peripheral blood specimens longitudinally collected between 3 weeks and one year after leukemia treatment, we examined single-cell mRNA sequencing (scRNA-seq) analysis of 16 HLA-matched patients receiving either Orca-T or unmanipulated PBSC grafts.
2026-03-01 | GSE290836 | GEO