Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Next Generation Sequencing Facilitates Quantitative Analysis of Osteoblast Mineralization Transcriptomes

ABSTRACT: We report the application of next generation sequencing technology for high-throughput profiling of mRNA, circRNA and lncRNA in hFOB 1.19 cells during the mineralization. Osteoblast RNA profiles in different process of mineralization, which is day 0, day 3, day 6 and day 9, respectively. The transcriptome sequencing on an Illumina HiSeq X Ten platform were carried out at Novogene Bioinformatics Technology Co., Ltd. (Beijing, China). Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. In the process of osteoblast mineralization, a total of 8464 dysregulated circRNAs were identified, of which 6332 circRNAs were upregulated and 2132 circRNAs were downregulated. In addition, 1633 differentially expressed mRNAs were also identified, with 1027 mRNAs upregulated and 606 mRNAs downregulated. This study provides a framework for the application of NGS profiling towards characterization of osteoblast mineraliztion.

ORGANISM(S): Homo sapiens

PROVIDER: GSE148203 | GEO | 2020/11/08

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

CHD1 regulates cell fate determination by activation of differentiation-induced genes

Project description:We describe here a novel role for CHD1 in regulating the osteoblast cell fate by studying the effect of CHD1 depletion on the epigenetic landscape and on mRNA expression in mesenchymal stem cells (MSC) (Simonsen et al. 2012) and fetal Osteoblast (hFOB 1.19) (Harris et al. 1995) during osteoblast differentiation.

2017-09-03 | GSE89179 | GEO

Homo sapiens

Project description:Human osteoblast- (hFOB 1.19 (ATCC CRL-1137) Transcriptome

| PRJNA448221 | ENA

osteoblast mineralisation

Project description:Bone mineralization is a carefully orchestrated process, regulated by a number of promoters and inhibitors that function to ensure effective hydroxyapatite formation. Here we sought to identify new regulators of this process through a time series microarray analysis of mineralising primary osteoblast cultures over a 27 day culture period.

2012-12-01 | E-MTAB-1391 | biostudies-arrayexpress

Dissection of estrogen receptor alpha signaling pathways in osteoblasts using RNA-sequencing

Project description:The goal is to identify estrogen-dependent gene expression patterns using RNAseq for 3 different ERα forms in human osteoblasts. We analyzed 3 different forms of estrogen receptor alpha (ERα), 1) Wild-type, 2) NERKI (DNA-binding mutant) and 3) NOER (Nuclear Only ERα, not membrane). Each was infected into hFOB (human osteoblast) cells and treated with either vehicle or E2 (10nM) (n=3 for each group/treatment). RNAseq was then performed.

2015-03-11 | E-GEOD-55769 | biostudies-arrayexpress

Rattus norvegicus

Project description:Effect of polyphosphates on osteoblast mineralization

| PRJDB4598 | ENA

Rattus norvegicus

Project description:Effect of polyphosphates on osteoblast mineralization

| PRJNA315105 | ENA

A time series study on BMP6 induced osteoblast differentiation of human mesenchymal stem cells (hMSC)

Project description:BMP6 mediated osteoblast differentiation plays a key role in skeletal development and bone disease. Unfortunately, the signaling pathways regulated by BMP6 are largely uncharacterized due to both a lack of data and the complexity of the response. To better characterize the signaling pathways responsive to BMP6, we conducted a time series microarray study to track BMP6 induced osteoblast differentiation and mineralization. Human MSC cells underwent osteogenic induction with BMP6 treatment for 0 hours, 8 hours, 24 hours, and 96 hours, which correspond to four phenotypic groups, i.e. control, preosteoblast (no mineralization), (sub-maximal) mineralization, and maximal mineralization at 14 days after the initiation of BMP treatment (18 days in total). Cells were harvested at 8 hours, 24 hours, 96 hours and 10 days for microarray profiling. Assays were run in duplicate for a total of 26 arrays. We only used 20 arrays in the reference paper.

2011-09-19 | E-GEOD-28074 | biostudies-arrayexpress

Expression data from primary murine pre-osteoblasts from control and Il15ra knockout mice

Project description:Interleukin-15 receptor alpha (IL15RA) is an important component of interleukin-15 (IL15) pro-inflammatory signaling. In addition, IL15 and IL15RA are present in the circulation and are detected in a variety of tissues where they influence physiological functions such as muscle contractility and overall metabolism. In the skeletal system, IL15RA was previously shown to be important for osteoclastogenesis. Little is known, however, about its role in osteoblast function and bone mineralization. In this study, we evaluated bone structural and mechanical properties of an Il15ra whole-body knockout mouse (Il15raKO) and used in vitro and bioinformatic analyses to understand the role IL15/IL15RA signaling on osteoblast function. We show that lack of IL15RA decreased bone mineralization in vivo and in isolated primary osteogenic cultures, suggesting a cell-autonomous effect. Il15raKO osteogenic cultures also had reduced Rankl/Opg mRNA ratio, indicating defective osteoblast/osteoclast coupling. We analyzed the transcriptome of primary pre-osteoblasts from normal and Il15raKO mice and identified 1150 genes that were differentially expressed at an FDR of 5%. Of these, 844 transcripts were upregulated and 306 were downregulated in Il15raKO cells. The largest functional clusters, highlighted using DAVID analysis, were related to metabolism, immune response, bone mineralization and morphogenesis. The transcriptome analysis was validated by qPCR of some of the most significant hits. Using bioinformatic approaches, we identified candidate genes, including Cd200 and Enpp1, that could contribute to the reduced mineralization. Silencing Il15ra using shRNA in the calvarial osteoblast MC3T3-E1 cell line decreased ENPP1 activity. Taken together, these data support that IL15RA plays a cell-autonomous role in osteoblast function and bone mineralization.

2017-07-05 | GSE99414 | GEO

Gene expression changes in 786-O cells in response to Everolimus, SGI-1027, or their combination.

Project description:Renal cell carcinoma (RCC) is one of the most common malignant tumors of urinary system. The Food and Drug Administration (FDA) has approved everolimus for the treatment of advanced RCC, but r everolimus resistance limits its application in clinic. We here reported the DNA methyltransferase 1 (DNMT1) inhibitor SGI-1027 as an inducer of methuosis, a type of cell death form independent of apoptosis. Additionally, SGI-1027 and everolimus worked in concert to suppress the proliferation, migration, and invasion of renal cancer cells while also inducing apoptosis and GSDME-dependent pyroptosis. In vitro transplanted tumor mice models, everolimus combined with SGI-1027 played a significant inhibitory effect on the growth of renal cancer tumors with good tolerance. The objective of this study is to explore the mechanism of the synergistic effect of everolimus and SGI-1027. We demonstrated through analysis of transcriptome high-throughput sequencing data that lysosomes were strongly linked with the synergistic effect of everolimus and SGI-1027 at the transcriptional level, which provides a new strategy for everolimus resistance and the treatment of advanced RCC.

2024-10-23 | GSE242110 | GEO

High-throughput sequencing for lacrimal sacs from chronic dacryocystitis patients and normal controls

Project description:We report the application of whole transcriptome sequencing technology for high-throughput profiling of lacrimal sacs from chronic dacryocystitis patients and normal controls. Differently expressed mRNAs and circRNAs were used for co-expression analysis. The expression levels of mRNAs and circRNAs in control and chronic dacryocystitis samples were validated by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Among all the 3909 circRNAs predicted from RNA sequencing data, 25 circRNAs (20 up regulated and 5 down-regulated) were differentially expressed in chronic dacryocystitis samples. Besides, 1486 differentially expressed mRNAs were identified. This study identified statistically significant differences between circRNAs and mRNAs of lacrimal sac samples of chronic dacryocystitis patients and control individuals. Of these differently expressed circRNAs and mRNAs, eight were validated by qRT-PCR, including MYH2, DSP, CD27, CCL5, FN1, has_circ_0004792, has_circ_0001062 and has_circ_0115476. This study suggested the differentially expressed circRNAs might participate in pathogenesis of chronic dacryocystitis, and it is therefore reasonable to consider circRNAs as potential therapeutic targets in treating chronic dacryocystitis patients.

2024-11-15 | GSE188810 | GEO

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