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Understanding the functional role of cyanidin-3-O-glucoside in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis

ABSTRACT: Understanding the functional role of cyanidin-3-O-glucoside in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis

PROVIDER: PRJNA629814 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR11680620_1.fastq.gz	Fastqsanger.gz
	SRR11680620_2.fastq.gz	Fastqsanger.gz
	SRR11680621_1.fastq.gz	Fastqsanger.gz
	SRR11680621_2.fastq.gz	Fastqsanger.gz
	SRR11680622_1.fastq.gz	Fastqsanger.gz

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Understanding the functional role of cyanidin-3-O-glucoside in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis

Project description:Cyanidin-3-O-glucoside (C3G) is one of the most widely distributed anthocyanins and has the effect of reducing the risks of osteoporosis. However, the molecular mechanism by which C3G promotes bone formation remains incompletely understood. Our aim was to investigate the effect of C3G on gene expression profiles, during the proliferation and differentiation in MC3T3-E1, a kind of osteoblast cell line from mice, by RNA sequencing. The results identified 34 up-regulated and 17 down-regulated genes. We further performed Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes analyses (KEGG), and other bioinformatics methods to do further analysis of differentially expressed genes (DEGs). Analysis of sequencing data showed that these genes were highly enriched in functions related to Lysosomal and Glycolipid biosynthetic. Lastly, we used RT-qPCR to validate the differentially expressed mRNAs. The results showed that C3G increased the expression levels of Ly6a (Lymphocyte antigen 6 family member A), Atp6v0c (ATPase H+ transporting v0 subunit c), and decreased the expression levels of Cx3cl1 (C-X3-C motif chemokine ligand 1). This study suggested that C3G activated osteoblast via Glycosylphosphatidylinositol(GPI)-anchor biosynthesis and the Cx3cl1/Cx3cr1 signaling pathway.

2022-10-19 | GSE149731 | GEO

Effects of Hsd11b1 overexpressing in mc3T3-e1 pre-osteoblastic cell lines under glucocorticoid excess

Project description:To explore the mechanism by which osteoblastic 11β-HSD1 regulates bone formation and glucose handling, we transfected the mouse MC3T3-E1 osteoblastic cells with a plasmid carrying the exogenous Hsd11b1 or EGFP gene to construct the 11β-HSD1-overexpressed and control osteoblastic cells (hereafter MC3T3-HSD1 and MC3T3-GFP cells), respectively. After incubating with 11-DHC,we then employed RNA sequencing (RNA-seq) to examine the gene expression profile between MC3T3-HSD1 and MC3T3-GFP cells.

2024-09-25 | GSE274790 | GEO

Effects of Hsd11b1 overexpressing in mc3T3-e1 pre-osteoblastic cell lines under glucocorticoid excess (ATAC-Seq)

Project description:To explore the mechanism by which osteoblastic 11β-HSD1 regulates bone formation and glucose handling, we transfected the mouse MC3T3-E1 osteoblastic cells with a plasmid carrying the exogenous Hsd11b1 or EGFP gene to construct the 11β-HSD1-overexpressed and control osteoblastic cells (hereafter MC3T3-HSD1 and MC3T3-GFP cells), respectively. After incubating with 11-DHC,we then employed assay for transposase-accessible chromatin with sequencing (ATAC-seq) to examine the gene expression profile between MC3T3-HSD1 and MC3T3-GFP cells.

2024-09-25 | GSE274974 | GEO

Search for PTH-induced genes in MC3T3-E1 cells

Project description:To identify the changes of mRNA expressions by PTH-treatment for 1 hr in mouse osteoblastic cell line MC3T3-E1, we performed RNA-sequencing (RNA-seq).

2024-06-21 | GSE231552 | GEO

Comparison of gene expression profiles between MC3T3-E1 without osteoblastic induction and with 14 days of ostoblastic induction

Project description:Microarray study revealed 1324 genes that were up-regulated and 1550 genes that were down-regulated more than 1.5 fold change (corrected p<0.05) in MC3T3-E1-derived-mature Osteoblasts compared to control MC3T3-E1.

2019-04-21 | GSE46400 | GEO

Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1

Project description:Purpose: This is a post-GWAS functional study that aims to determine the effect of Akap11 knockout in mouse preosteoblastic cell line MC3T3-E1 during osteogenesis. Methods: mRNA profile of WT (treated with CRISPR and remains unedited) and Akap11 knockout MC3T3-E1 cells were generated by RNAseq from pooled RNA (from 3 biological triplicate at equal quantity) of various timepoint during osteogenesis (Day 0, 7,16, 25).100ng total RNA was used for library construction by KAPA Stranded mRNA-Seq Kit (Roche). Pair-End 101bp sequencing was performed in the Illumin HiSq1500 sequencer using the HiSeq SBS Kit v4 (Illumina). Data was collected with SCS version 1.4.8. Base calling was performed using Illumina’s RTA (Version 1.12.4.2). 7 samples were sequenced per lane and achieved a sequencing depth of ~65 million read per sample. Results: Expression of osteogentic markers in Akap11 knockout MC3T3-E1 cells were suppressed. Genes invovled in IGF-I signaling pathway were signficantly altered.

2019-08-30 | GSE136591 | GEO

Genomic characterization of osteoblastic differentiation of MC-3T3E1 cells

Project description:Gene expression analysis of murine MC3T3-E1 cells induced to undergo synchronized osteoblastic differentiation in vitro.

2012-06-28 | GSE30393 | GEO

Expression Data from MC3T3-E1 cells subjected to laminar fluid flow (LFF)

Project description:Osteoblasts are responsive to shear stress. We investigated the effect of of laminar fluid flow (LFF) on osteoblast-like MC3T3-E1 cells at two timepoints. We used microarray analysis to detail the global gene expression of MC3T3-E1 cells in response to 1 hour of laminar fluid flow directly and 4 hours after treatment.

2021-02-15 | GSE138160 | GEO

Identification of differentially expressed genes associated with dimethyl sulfoxide-enhanced mineralization in mouse MC3T3-E1 preosteoblast cells.

Project description:Dimethyl sulfoxide (DMSO) is widely used as a solvent for water-insoluble substances and has biological properties such as inducing cellular differentiation, scavenging free radicals, and acting as a radioprotectant. DMSO has also been reported to enhance mineralization in osteoblastic cells. However, its molecular mechanisms have not yet been fully elucidated. In this study, we identified the differentially expressed genes associated with dimethyl sulfoxide-enhanced mineralization in mouse MC3T3-E1 preosteoblast cells using GeneChip® oligonucleotide microarrays.

2024-08-12 | GSE274013 | GEO

Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1

Project description:Akap11 is a positive regulator of osteogenesis in mouse osteoblastic cell line MC3T3-E1

| PRJNA562822 | ENA