Ontology highlight
ABSTRACT:
PROVIDER: PRJEB34399 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
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| ERR3518148.fastq.gz | Fastqsanger.gz |
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Project description:No.1 Vehicle control. Bone marrow derived macrophages were treated with vehicle control for 30 mins. Cells were then lysed and alkylated by IAM, followed by immunoprecipitation of STING protein and gel separation of the protein. After digestion and secondary alkylation by NEM, sample was submitted for MS analysis. No.2 Menadione treated sample. Bone marrow derived macrophages were treated with Menadione for 30 mins. Cells were then lysed and alkylated by IAM, followed by immunoprecipitation of STING protein and gel separation of the protein. After digestion and secondary alkylation by NEM, sample was submitted for MS analysis.
2020-05-12 | MSV000085403 | MassIVE
Project description:Mice were euthanized at 20 weeks of age, and humeri were obtained for metabolomic analyses. Once obtained, marrow was flushed in some humeri resulting in 3 sample types including whole bone, bone marrow, and isolated cortical bone. Metabolites were extracted and underwent LC-MS analysis using an Agilent LC 1290 coupled to an Agilent 6538 QTOF
2022-04-21 | ST002147 | MetabolomicsWorkbench
Project description:We cultured bone marrow derived dendritic cells from WT and CD11c KO mice. Then, a group of bone marrow dendritic cells were stimulated with LPS overnight. We obtained bone marrow derived dendritic cells with or without LPS stimulation and analyzed proteomics profiles.
2024-01-26 | PXD048907 |
Project description:sorted hematopoetic stem cells from bone marrow; with two rounds of amplification Keywords: repeat sample
2004-09-30 | GSE693 | GEO
Project description:Vitamin A is the only known compound that produces spontaneous fractures in rats. In an effort to resolve the molecular mechanism behind this effect, we fed young rats high doses of vitamin A and performed a global transcriptional analysis of diaphyseal bone after one week, i.e. just before the first fractures appeared. Microarray gene expression analysis revealed that 68 transcripts were differentially expressed in hypervitaminotic cortical bone and 118 transcripts were found when the bone marrow was also included. 98% of the differentially expressed genes in the bone marrow sample were up-regulated. In contrast, hypervitaminotic cortical bone without marrow showed reduced expression of 37% of differentially expressed genes. Gene Ontology (GO) analysis revealed that only samples containing bone marrow were associated to a GO term, which principally represented extracellular matrix (ECM). This is consistent with the histological findings of increased endosteal bone formation. Four of the genes in this ECM cluster and four other genes, including Cyp26b1 which is known to be up-regulated by vitamin A, were selected and verified by real-time PCR. In addition, immunohistochemical staining of bone sections confirmed that the bone-specific molecule, osteoadherin (Omd) was up-regulated. Further analysis of the major gene expression changes revealed distinct differences between cortical bone and bone marrow, e.g. there appeared to be augmented Wnt signaling in the bone marrow but reduced Wnt signaling in cortical bone. Moreover, induced expression of hypoxia-associated genes was only found in samples containing bone marrow. Together, these results corroborate our previous observations of compartment-specific effects of vitamin A, with reduced periosteal but increased endosteal bone formation, and suggest important roles for Wnt signaling and hypoxia in the processes leading to spontaneous fractures.
2011-12-21 | GSE29859 | GEO
Project description:Microarray analysis of mouse bone marrow hematopoietic progenitors after bone marrow transplant
| PRJNA950383 | ENA
Project description:FLT3+/CD11b+ Dendritic cell (DC) progenitor was amplified in vitro from mouse bone marrow. Keywords: repeat sample
2004-09-30 | GSE692 | GEO
Project description:Purpose: The goals of this study are to compare the transcriptome profile of mouse hematopoietic stem/progenitor cells (HSPC) from the bone marrow overexpressing the innate immune adaptor protein TIRAP to control vector expressing HSPC using RNA-Seq. Methods: mRNA profiles of wild-type (WT) mice bone marrow overexpressing TIRAP or control vectors were generated by deep sequencing, in triplicate, using the Illumina platform. RNA-Seq data were aligned using JAGuaR (v2.0.3), using the mm10 reference. Expression quantification was performed with Sailfish (v0.6.2), using RefSeq gene models. The differential expression analysis between TIRAP expressing bone marrow and control was performed using DESeq2 (v1.10.1). Results: Using an optimized data analysis workflow, we mapped approximately 92% sequenced reads on average per sample to the mouse genome (build mm10).
2022-01-04 | GSE172147 | GEO
Project description:<p>This study analyzed samples from 29 patients with juvenile myelomonocytic leukemia (JMML) using whole exome sequencing. Each patient had a paired germline tissue along with a diagnostic leukemia sample. Germline tissue types included buccal mucosa, cordblood, Epstein-Barr virus immortalized cell lines and fibroblasts from either skin or bone marrow. Leukemia samples were either blood or bone marrow. Seven of the 29 patients also had a relapsed leukemia sample available for exome analysis.</p>
| phs000973 | dbGaP
Project description:The paper describes a model of tumor invasion to bone marrow.
Created by COPASI 4.26 (Build 213)
This model is described in the article:
Modeling invasion of metastasizing cancer cells to bone marrow utilizing ecological principles
Kun-Wan Chen, Kenneth J Pienta
Theoretical Biology and Medical Modelling 2011, 8:36
Abstract:
Background: The invasion of a new species into an established ecosystem can be directly compared to the steps involved in cancer metastasis. Cancer must grow in a primary site, extravasate and survive in the circulation to then intravasate into target organ (invasive species survival in transport). Cancer cells often lay dormant at their metastatic site for a long period of time (lag period for invasive species) before proliferating (invasive spread). Proliferation in the new site has an impact on the target organ microenvironment (ecological impact) and eventually the human host (biosphere impact).
Results: Tilman has described mathematical equations for the competition between invasive species in a structured habitat. These equations were adapted to study the invasion of cancer cells into the bone marrow microenvironment as a structured habitat. A large proportion of solid tumor metastases are bone metastases, known to usurp hematopoietic stem cells (HSC) homing pathways to establish footholds in the bone marrow. This required accounting for the fact that this is the natural home of hematopoietic stem cells and that they already occupy this structured space. The adapted Tilman model of invasion dynamics is especially valuable for modeling the lag period or dormancy of cancer cells.
Conclusions: The Tilman equations for modeling the invasion of two species into a defined space have been modified to study the invasion of cancer cells into the bone marrow microenvironment. These modified equations allow a more flexible way to model the space competition between the two cell species. The ability to model initial density, metastatic seeding into the bone marrow and growth once the cells are present, and movement of cells out of the bone marrow niche and apoptosis of cells are all aspects of the adapted equations. These equations are currently being applied to clinical data sets for verification and further refinement of the models.
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2024-09-02 | BIOMD0000000793 | BioModels