Ena-DATASET-IJC-07-11-2014-17:58:39:549-794 - samples
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA254802
PROVIDER: EGAD00001001058 | EGA |
REPOSITORIES: EGA
Publications
Role of casein kinase 1A1 in the biology and targeted therapy of del(5q) MDS.
Schneider Rebekka K RK Ademà Vera V Heckl Dirk D Järås Marcus M Mallo Mar M Lord Allegra M AM Chu Lisa P LP McConkey Marie E ME Kramann Rafael R Mullally Ann A Bejar Rafael R Solé Francesc F Ebert Benjamin L BL
Cancer cell 20140918 4
The casein kinase 1A1 gene (CSNK1A1) is a putative tumor suppressor gene located in the common deleted region for del(5q) myelodysplastic syndrome (MDS). We generated a murine model with conditional inactivation of Csnk1a1 and found that Csnk1a1 haploinsufficiency induces hematopoietic stem cell expansion and a competitive repopulation advantage, whereas homozygous deletion induces hematopoietic stem cell failure. Based on this finding, we found that heterozygous inactivation of Csnk1a1 sensitiz ...[more]
Similar Datasets
Project description:Copy number status of 39 human AML samples was analyzed using CytoChip Cancer 4x180K v2.0 microarray chips from BlueGnome. Half the samples represent de novo AMLs while the other half represents secondary AMLs. Sample material consisted of cryopreserved bone marrow or blood aspirates. DNA was purified using the Gentra Puregene Blood Kit (Qiagen Nordic, Solna, Sweden) according to protocol. The test samples were labelled with Cy3 and the reference samples, consisting of sex-matched genomic DNA (Promega, Madison, WI, USA), were labelled with Cy5. The arrays were processed according to the manufacture’s recommendations using 0.5-1.0 µg of DNA as input material for each labelling reaction. The processed microarrays were scanned at 532 and 635 nm using a GenePix 4400A laserscanner (Molecular Devices, Winnersh, UK) at a resolution of 2.5 µm and GenePix Pro 7.0 software (Molecular Devices). The resultant image files were analyzed in BlueFuse Multi 3.1. using the Cytochip v2 algorithm. This software does not provide raw data files but only the processed data for each hybridization. Therefore, no raw data files are attached to this experiment.
2020-12-31 | E-MTAB-3663 | biostudies-arrayexpress
Project description: Not available
| S-EPMC4284207 | biostudies-literature
Project description:The origin of bone marrow stromal cells (BMSCs) is not completely understood. We have identified a rare population of cells with a transcriptional profile consistent with endothelial to mesenchymal transition (Endo-MT) in human fetal development. Therefore, we hypothesized that Endo-MT contributes to bone marrow niche formation in mammals. Here, we sought to determine whether Endo-MT cells could be identified in murine bone marrow during embryonic development. We isolated bone marrow and collagenased bone fraction from long bones of 9 fetuses at embryonic day 17 (E17) and FACS purified endothelial cells and BMSCs for single cell RNA sequencing.
2021-01-21 | E-MTAB-9994 | biostudies-arrayexpress
Project description:Background and aimsThis study aimed to evaluate the factors associated with addictive behavior and mental health in adolescents aged 11-17 years in Bangladesh.MethodsThis study analyzed data from the Bangladesh Global School-based Health Survey (GSHS) conducted in 2014. Adolescents aged 11-17 years studying government schools were considered as respondents for this survey. A two-phase group sample design was utilized to deliver illustrative information of all understudies in grades (classes) 7-10 in Bangladesh. Bivariate analyses followed by a weight-adjusted multiple logistic regression was fitted to a sample of size 2989 adolescents.ResultsOne in ten and one in four adolescents had different substance addictions and some forms of mental health conditions, respectively. Sex of participants (adjusted odds ratio [AOR]: 4.49; confidence interval [CI]:2.28-8.84), being bullied (AOR: 3.08; CI:1.46-6.49), use of tobacco among parents (AOR: 5.82; CI:3.16-10.75), parental understanding of adolescents' problems (AOR: 0.45; CI:0.23-0.82), and food affordability (AOR: 1.24; CI:1.09-1.42) were associated with addictive behaviors of adolescents. Bullied males with nonempathetic parents were found to be more vulnerable to addictive behaviors and bullied females showed higher tendencies to mental health issues.ConclusionConsidering the elevated prevalence of reported mental health concerns, identifying vulnerable groups and formulating intervention-oriented policies engaging youths can pave the way towards achieving robust health and well-being for them in Bangladesh.
| S-EPMC11222289 | biostudies-literature
Project description: Not available
| S-EPMC4305153 | biostudies-literature
Project description:To identify the mediators of phagocytosis of living cells upregulated by the triple stimuli, we examined the gene expression profiles of BMDMs(Bone-marrow derived macrophages) with microarray consisting of about 40,000 mouse genes
2017-09-18 | GSE90881 | GEO
Project description:'miRNA expression in 39 human AML samples was analyzed on Sureprint G3 Human miRNA (release 16.0) 8x60K Microarrays from Agilent Technologies. Half the samples represent primary AMLs while the other half represents secondary AMLs. Sample material consisted of cryopreserved bone marrow or blood aspirates. RNA from the samples was purified using the miRNeasy Mini Kit from Qiagen and the sample quality was tested on a Bioanalyser (all sample had RIN values ≥6.0 [mean=8.4]). The samples were labelled with Cy3 and processed according to Agilent''s protocol using vacuum concentration to dry the samples before microarray hybridization. The processed microarrays were scanned at 532 nm using a GenePix 4400A laserscanner at a resolution of 2.5 µm and the GenePix Pro 7.0 software.'
2020-12-31 | E-MTAB-3627 | biostudies-arrayexpress
Project description:Chemical investigation of cyanobacterial strain HT-58-2, which most closely aligns with the genus Brasilomena, has led to the isolation of two compounds related to tolypodiol. The structures and absolute configuration of 6-deoxytolypodiol (1) and 11-hydroxytolypodiol (2) were elucidated by spectroscopic and spectrometric analysis. While tolypodiol previously showed anti-inflammatory activity in a mouse ear edema assay, only 2 reduced in vitro thromboxane B2 and superoxide anion (O2-) generation from Escherichia coli lipopolysaccharide-activated rat neonatal microglia to any appreciable degree.
| S-EPMC7246299 | biostudies-literature
Project description:Human biology is tightly linked to proteins, yet most measurements do not precisely determine their full sequence and post-translational modifications. Here, we present the primary structures of 30,000 unique proteoforms expressed from 1,690 human genes across 21 cell types and plasma from human blood and bone marrow compiled in the Blood Proteoform Atlas (BPA). Our results indicate that while a given protein can be expressed across multiple cell types, the proteoform functions as a more specific indicator of differentiation. These results provide a better biochemical description of protein-level biology expressed through gene transcription and translation. We demonstrate the utility of the BPA by focusing on cell- and proteoform-specific signatures within 58 liver transplant recipients having healthy graft function or undergoing acute organ rejection or dysfunction.
2023-09-07 | PXD045201 | Pride
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.
To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models .
To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide.
Please refer to CC0 Public Domain Dedication for more information.
2024-09-02 | BIOMD0000000795 | BioModels