Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

56 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Plasma profiling of miRNAs in mouse model of osteosarcoma.

ABSTRACT: Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from a genetically engineered mouse model of OS to identify a profile of four plasma miRNAs. Plasma from mice with OS were profiled for miRNAs and compared with the profile of plasma from disease-free mice

ORGANISM(S): Mus musculus

SUBMITTER: Chad Creighton

PROVIDER: E-GEOD-65236 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Plasma profiling of miRNAs in human specimens from osteosarcoma patients.

Project description:Osteosarcoma (OS) is the primary bone tumor in children and young adults. Currently, there are no reliable, non-invasive biological markers to detect the presence or progression of disease, assess therapy response, or provide upfront prognostic insights. Using a qPCR-based platform that analyzes more than 750 miRNAs, we analyzed control and diseased-associated plasma from human cases of OS to identify a profile of differentially expressed miRNAs. Comprehensive miRNA expression profiling was completed using the Exiqon miRNome platform (human panels I+II, V3) on 20 disease samples (10 localized, 10 metastatic) and 15 healthy controls.

2015-01-17 | E-GEOD-65071 | biostudies-arrayexpress

Mouse retina proteomics - Integrative subcellular proteomic analysis allows accurate prediction of human disease causing genes

Project description:Proteomic experiments were performed on the outer segment (OS) and the remaining retina (RR). For the OS proteomics, three biological replicates were performed for mouse at the age of P15, which included 24, 26 and 26 retinas respectively. We also performed the OS proteomic experiment on 40 retinas from mice at age P13. For the RR proteomic experiments, two biological replicates were performed independently using 30 and 30 retinas respectively.

2016-02-26 | PXD003441 | Pride

Proteomic profiling of plasma membrane proteins from bovine rod photoreceptor outer segments

Project description:The outer segment (OS) organelle of vertebrate photoreceptors is a highly specialized cilium whose plasma membrane plays vital and diverse roles in supporting photoreceptor function and health. However, little is known about the identity of its protein constituents, as this membrane cannot be purified to homogeneity. In this study, we employed the technique of protein correlation profiling to identify unique OS plasma membrane proteins. To achieve this, we used label-free quantitative mass spectrometry to compare relative protein abundances in an enriched preparation of the OS plasma membrane to a preparation of total outer segment membranes. We have found that only five proteins were enriched at the same level as previously validated OS plasma membrane markers. Two of these proteins, TMEM67 and TMEM237, had not been previously assigned to this membrane and one, embigin, had not been identified in photoreceptors. We further showed that embigin associates with monocarboxylate transporter MCT1 in the OS plasma membrane, facilitating lactate transport through this cellular compartment.

2021-04-30 | PXD022864 | Pride

Real-time PCR analysis of microRNA expression in differentiating human skeletal muscle cells

Project description:Human skeletal myoblast cell line LHCN-M2 (Zhu et al., Aging Cell (2007), vol. 6, pp 515-523) were plated on collagen-coated 6-well Falcon cell culture plates at 500 000 cells/well, differentiation was induced 24h later by switching to DMEM supplemented with 0,01 mg/ml insulin and 0,1 mg/ml transferrin. Cells were collected at 0, 3, and 7 days of differentiation time points. Total RNA was extracted and miRNA expression evaluated by quantitative real-time PCR. MiRNA expression profiling in proliferating and differentiating (3 and 7 days) human skeletal myoblasts LHCN-M2.

2013-04-11 | E-GEOD-45957 | biostudies-arrayexpress

Plasma microRNA profiles in women with and without endometriosis at different menstrual cycle phases

Project description:The objectives of the study: 1. Does the phase of the menstrual cycle alter microRNA (miRNA) plasma profiles in healthy women of reproductive age and in women with endometriosis? 2. Does this alter prospects for development of a miRNA-based diagnostic test for endometriosis? Prospectively recruited asymptomatic control women and women with surgically diagnosed endometriosis (n = 8 in each group) were included. Each patient provided blood samples in the early proliferative, late proliferative and mid luteal phases of the menstrual cycle (n = 47 total plasma samples). The cycle phase was verified by hormonal profile. RNA was extracted from each sample and expression of microRNAs was assessed using TaqMan Low Density Human miRNA arrays.

2013-05-09 | E-GEOD-46735 | biostudies-arrayexpress

Transcription profiling of human osteosarcoma Sa OS cells vs reference RNA of human osteosarcoma U-2 OS cells

Project description:Osteosarcoma (OS) is a common primary bone malignancy that is characterized by high degree of aneuploidy, gene amplification, and multiple unbalanced chromosomal rearrangements. The human osteosarcoma U-2 OS and Sa OS cells lines have been generated more than three decades ago and are used in a wide spectrum of biomedical research. Nevertheless, and despite scattered information about their genetic context, no comprehensive comparative study of their transcriptome profile has been reported to date. The aim of this study was to elucidate common molecular characteristics of the two cell lines as well as differences in their expression profile. Thus the genome wide gene expression profile of the Sa OS cells was compared with reference RNA of U-2 OS cells. These results may provide the basis for future studies and illuminate the molecular differences of the two widely used cell lines.

2009-09-21 | E-MEXP-1897 | biostudies-arrayexpress

miRNA gene expression profiles from osteosarcoma samples and cell lines

Project description:Although the introduction of combined neoadjuvant chemotherapy has significantly prolonged the survival, the outcome of OS patients with poor response to chemotherapy is still unfavorable. To develop new therapeutics the elucidation of the entire molecular pathway regulating OS cell proliferation is warranted. We analysed the expression levels of 933 miRNA probes in surgical 24 samples and 8 cell lines of osteosarcoma with 3D-Gene human miRNA oligo chips. Total RNA was extracted from 24 fresh frozen tumour specimens and 8 OS cell lines. We analysed the global miRNA exprssion profiles of these osteosarcoma cases in order to find new novel potential targets for the development of therapeutic targeting OS.

2012-09-01 | E-GEOD-30934 | biostudies-arrayexpress

Modeling tumor subtypes in vivo using lineage restricted transgenic shRNA

Project description:Expression analysis from two genetically engineered mouse models of osteosarcoma determine the expression profile of mouse osteosarcoma Human osteosarcoma (OS) is comprised of three different subtypes: fibroblastic, chondroblastic and osteoblastic. We previously generated a mouse model of fibroblastic OS by conditional deletion of p53 and Rb in osteoblasts. Here we report an accurate mouse model of the osteoblastic subtype using shRNA-based suppression of p53. Like human OS, tumors frequently present in the long bones and preferentially disseminate to the lungs; features less consistently modeled using Cre:lox approaches. Our approach allowed direct comparison of the in vivo consequences of targeting the same genetic drivers using different technology. This demonstrated that the effects of Cre:lox and shRNA mediated knock-down are qualitatively different, at least in the context of osteosarcoma. Through the use of complementary genetic modification strategies we have established a model of a distinct clinical subtype of OS that was not previously represented and more fully recapitulated the clinical spectrum of this human tumor. 4 primary tumors from Cre:lox OS model; 4 primary tumors from shRNA OS model.

2013-03-28 | E-GEOD-38742 | biostudies-arrayexpress

Development of a mass spectrometric method for the analysis of periplasmic proteins from Gram-negative bacteria

Project description:Mass spectrometry-based proteomics has emerged as a powerful technique in the field of clinical diagnostics but requires a multistep process for sample preparation. The purpose of clinical mass spectrometry is to detect and quantify protein targets using well-established methods. Here, we found that the osmotic shock (OS) process allowed us to reduce the salt concentration and simultaneously enrich periplasmic proteins, specifically target proteins associated with antibiotic resistance in Gram-negative bacteria. Furthermore, we demonstrated that an optimized condition of the OS lysis allows the highest sensitivity in the MS analysis, and the OS lysate containing the proteins of interest (e.g., KPC-2) can be directly injected into multiple mass spectrometers without desalting process. Our study provides a detergent-free, straightforward method for periplasmic protein analysis using mass spectrometry.

2023-09-06 | PXD025999 | Pride

Transcriptional perturbations caused by SV40 large T antigen and its fragments

Project description:The small genome of polyomaviruses encodes a limited number of proteins that are highly dependent on interactions with host cell proteins for efficient viral replication. The SV40 large T antigen (LT) contains several discrete functional domains that contribute to the viral life cycle, including the DNA binding and helicase domains. In addition, the LT the C-terminal region is required for lytic infection in certain restrictive cell types. To understand how LT affects the host cell to facilitate viral replication, we expressed full-length or functional domains of LT in cells and identified interacting cellular proteins and performed expression profiling. LT perturbed the expression of p53 target genes and subsets of cell-cycle dependent genes regulated by the DREAM and the B-Myb-MuvB complexes. To examine transcriptome perturbations directly in human cells, we generated expression constructs of each LT fragment. Full length and truncated LT containing N-terminal HA and FLAG epitope tags were expressed from the pMSCV retroviral vector and introduced into U-2 OS cells. Total RNA was isolated from three biological replicate U-2 OS stable cell lines and gene expression was assayed on Affymetrix Human Gene U133 Plus 2.0 arrays.

2012-10-26 | E-GEOD-40567 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data