2021 Fiscal Year Research-status Report
Trans-omics analysis of the difference between Cortical and Trabecular bone.
| Project/Area Number |
21K09998
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| Research Institution | Niigata University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
加来 賢 新潟大学, 医歯学系, 准教授 (30547542)
魚島 勝美 新潟大学, 医歯学系, 教授 (50213400)
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| Project Period (FY) |
2021-04-01 – 2024-03-31
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| Keywords | trans-omics / extracellular matrix / bone phenotype / bone regeneration |
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| Outline of Annual Research Achievements |
In this experiment, the bioinformatic approach using trans-omics and the Matrisome database are being used to analyze the difference in the ECM composition and the regulatory networks of cortical and trabecular bone.
During this period, the Bioinformatics components, such as, installation of the R software, setting of the RNA sequencing environment and implementing the WGCNA (Weighted gene co-expression network analysis) packages were accomplished. RNA sequencing trials were performed. Data QC of FASTQ files was performed using the "Bioconductor" package of the Anaconda software. Read trimming was performed with the “Trimmomatic” software package, read alignment with the “Star” package, the Reference genome from Mus-musculus was obtain as well as partial analysis of the read counts.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
Progressing Rather Smoothly
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| Strategy for Future Research Activity |
Identification of the molecular cues that distinguish the bone type and analysis of ECM protein profile that distinguishes the bone type.
Samples of Cortical and trabecular bone will be isolated, dissected into pieces, decalcified, and solubilized by 8M Urea solution at 4C. Mass Spectrometry will be performed, and samples will be deglycosylated, digested into peptides, and applied to the LC-MS/MS (Liquid chromatography/tandem mass spectrometry) (use Core-facility at Niigata Univ.) Obtained spectra will be annotated with the UniProt database. All identified proteins will be further curated by the Matrisome database. From here, the relevant ECM composition associated with bone phenotype will be selected.
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| Causes of Carryover |
For the identification of the molecular cues that distinguish the bone type, trials on the RNA-seq data were processed by using R software with limited samples. The number of samples will be expanded for the next fiscal year according to plan.
Cortical and trabecular bone of mice C57BL/6J (Male, 8w) will be isolated from both side of femur; cortical bone from metaphysis and trabecular bone from diaphysis. Total RNA will be isolated using TRIzol reagent, by directly immerse the sample. Total RNA will be isolated and run for RNA-seq (outsourcing).
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