Canine Blood ChIP-seq
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA687509 | ENA |
REPOSITORIES: ENA
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Project description:Identification of canine regulatory regions in peripheral blood mononuclear cells from purebred dogs.
2021-04-13 | GSE163779 | GEO
Project description:Estrogen Receptor alpha (ERα) is a key driver of most breast cancers, and it is the target of endocrine therapies used in the clinic to treat women with ERα positive (ER+) breast cancer. The two methods ChIP-seq (chromatin immunoprecipitation coupled with deep sequencing) and RIME (Rapid Immunoprecipitation of Endogenous Proteins) have greatly improved our understanding of ERα function during breast cancer progression and in response to anti-estrogens. A critical component of both ChIP-seq and RIME protocols is the antibody that is used to pull down the bait protein. To date, most of the ChIP-seq and RIME experiments for the study of ERα have been performed using the sc-543 antibody from Santa Cruz Biotechnology. However, this antibody has been discontinued, thereby severely impacting the study of ERα in normal physiology as well as diseases such as breast cancer and ovarian cancer. Here, we compare the sc-543 antibody with other commercially available antibodies, and we show that 06-935 (EMD Millipore) and ab3575 (Abcam) antibodies can successfully replace the sc-543 antibody for ChIP-seq and RIME experiments.
2019-03-21 | PXD012930 | Pride
Project description:Circulating tumor cells in the peripheral have proven to be independent prognostic factors for overall survival the monitoring of therapeutic success of human breast cancer patients. Postmortem morphologic evidence also points towards the presence of circulating tumor cells in the peripheral blood of dogs with metastatic canine mammary tumors. However, the existence of these cells has not been verified in canines in vivo and they have not been isolated and characterized due to the lack of appropriate and canine specific detection methods. In the present study a panel of 73 genes with high expression levels in canine mammary carcinoma cells and but not in peripheral blood leukocytes were identified using microarray analysis. From this panel, six mRNA markers, AGR2, ATP8B1, CRYAB, F3 and IRX3, were expressed in canine mammary carcinoma cells but not in the peripheral blood of dogs. All six RT-PCR assays, were sensitive enough detect one carcinoma cell admixed in 106 or more peripheral blood leukocytes, a common concentration of circulating tumor cells in the peripheral blood of human breast cancer patients. These five mRNA markers may therefore be used to detect canine mammary circulating tumor cells and to study their spatio-temporal presence in the peripheral blood of canine patients.
2011-12-10 | GSE25586 | GEO
Project description:Circulating tumor cells in the peripheral have proven to be independent prognostic factors for overall survival the monitoring of therapeutic success of human breast cancer patients. Postmortem morphologic evidence also points towards the presence of circulating tumor cells in the peripheral blood of dogs with metastatic canine mammary tumors. However, the existence of these cells has not been verified in canines in vivo and they have not been isolated and characterized due to the lack of appropriate and canine specific detection methods. In the present study a panel of 73 genes with high expression levels in canine mammary carcinoma cells and but not in peripheral blood leukocytes were identified using microarray analysis. From this panel, six mRNA markers, AGR2, ATP8B1, CRYAB, F3 and IRX3, were expressed in canine mammary carcinoma cells but not in the peripheral blood of dogs. All six RT-PCR assays, were sensitive enough detect one carcinoma cell admixed in 106 or more peripheral blood leukocytes, a common concentration of circulating tumor cells in the peripheral blood of human breast cancer patients. These five mRNA markers may therefore be used to detect canine mammary circulating tumor cells and to study their spatio-temporal presence in the peripheral blood of canine patients. Two canine mammary carcinoma cell lines, CMM115 and CMM26, and peripheral blood samples of 3 healthy dog donors were used for microarray analysis. All blood donors were female, showed no signs of infectious or inflammatory disease and did not have mammary gland tumors or any other identifiable tumors at the time of collection. Furthermore, blood cell count and blood chemistry were unremarkable in all dogs.
2011-12-10 | E-GEOD-25586 | biostudies-arrayexpress
Project description:Canine DUXC isoforms and functional similarity to human DUX4 [ChIP-seq]
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Project description:5-aminolevulinic acid (ALA) is one of the natural amino acids and a product of the first heme synthesis pathway in mitochondria. Recently, a supplement containing ALA is available in Japan and used for the purpose of the enhancement of ATP synthesis via mitochondrial activity. In humans, the immunomodulatory effect of ALA has attracted attention as a new function of ALA, and its application to cancer, inflammatory disease, and autoimmune diseases are being investigated. In the present study, to evaluate the effects of ALA on canine immunity, we performed in vitro studies using peripheral blood mononuclear cells (PBMC) from healthy dogs. Heme oxygenase-1 protein was expressed in Madin-Darby Canine Kidney cells and PBMCs treated with 5-ALA and ferrous sodium citrate (SFC), which showed that ALA works in dogs as well as humans. When PBMCs were stimulated with concanavalin A (ConA), the addition of ALA resulted in a significant increase in interferon-gamma (IFN-γ) produced by ConA-stimulated PBMCs. A comprehensive genetic alteration using next-generation RNA sequences (RNA-seq) was performed. From the result of RNA-seq, ALA enhanced the gene expression of T cell immunity including Th1, Th2, and Th17 subsets. In particular, the IL-17 signaling pathway was significantly upregulated. Then, we confirmed that ALA promoted the production of interleukin (IL)-17A in ConA-stimulated PBMCs. Together, these findings reveal that ALA promotes heme synthesis in mitochondria and enhances ConA-induced T cell immune responses in canine PBMCs.
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Project description:RNA-Seq of canine osteosarcoma tumor samples obtained from Canine Comparative Oncology and Genomics Consortium
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Project description:We used single cell RNA sequencing (scRNA-seq) to characterize the heterogeneity of peripheral blood-derived canine iNKT cells relative to that of human iNKTs.
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Project description:The diversity of canine T cells is poorly understood. We used 5’ scRNA-seq coupled with immune repertoire sequencing to generate a highly detailed atlas of peripheral blood TCRαβ+ T cells of healthy dogs.
2023-03-01 | GSE218355 | GEO
Project description:Embryonic hematopoiesis is regulated by the coordinated interaction between transcription factors and the epigenetic regulators driving developmental-stage specific gene expression but how this process drives hematopoietic specification and terminal differentiation is poorly understood. Here we generated RNA-Seq, DNase-Seq and ChIP-Seq data for histone marks and transcription factors from ES-cell derived purified cells representing six sequential stages of blood cell specification and differentiation. Our data reveal the binding patterns of specific transcription factors involved in the priming and maintenance of distal elements and inform how binding impacts on promoter activity. Functional studies based on these data uncovered a previously unrecognised role for Hippo signalling in mammalian hematopoietic specification. Finally, we present a dynamic core regulatory network model for hematopoiesis and demonstrate its utility for the design of reprogramming experiments. Our study represents a powerful resource for studying hematopoiesis and demonstrates how such data can advance our understanding of mammalian development. ChIP-seq data of histone modifications and transcription factors, and RNA-seq data obtained from purified cells representing five sequential stages of murine blood cell specification and differentiation
2016-02-26 | E-GEOD-69096 | biostudies-arrayexpress