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| Status |
Public on Nov 16, 2018 |
| Title |
Identifying deer antler proliferation and mineralization genes using comparative RNA-seq |
| Organisms |
Homo sapiens; Dama dama |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: The goal of this study is to compare (RNA-seq) transcriptomes of in vitro cultured human bone marrow-derived mesenchymal stem cells (hMSCs) and fallow deer antler-derived skeletal progenitors (FD RM Cells) under multiple conditions to identify candidate proliferation and mineralization genes responsible for fast antler regeneration
Methods: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000. The sequence reads were analyzed at the transcript isoform level STARS followed by Cufflinks. Validation for genes of interest was performed using immunofluorescence staining.
Results: Comparison of human and fallow deer skeletal progenitor datasets yielded proliferation and mineralization gene candidates
Conclusions: Our study represents the first detailed analysis of human and fallow deer transcriptomes of skeletal progenitor cells under proliferation and mineralization conditions, with biologic replicates, generated by RNA-seq technology. Our in vitro comparative approach circumvent some of the logistical and technical challenges in identifying candidate proliferation and mineralization genes responsible for rapid deer antler regeneration. We conclude that in vitro comparison of RNA-seq based transcriptomes identified candidate proliferaiton and mineralization genes to advance bone biology and holds promise to rapidly regenerate large bone volumes for regenerative medicine. The comparative approach utilized here can be adapted for almost any tissue to study a specific phenomenon of interest.
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| Overall design |
Design: hMSCs and FD RM Cells were cultured in vitro under 1) serum-free (0% serum) or serum (10% serum) conditions for 2.5 days or 2) Control (0 ng/mL BMP-2 and 0 nM dexamethasone) and osteogenic (100 ng/mL BMP-2 and 100 nM dexamethasone) media for 24 days. mRNA profiles were generated by deep sequencing, in duplicate, using Illumina HiSeq 2000.
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| Contributor(s) |
Ker D, Wang D, Sharma R, Zhang B, Passarelli B, Neff NF, Li C, Maloney W, Quake S, Yang YP |
| Citation(s) |
30376879 |
| Submission date |
Nov 14, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter Yang |
| Organization name |
Stanford University
|
| Department |
Orthopaedic Surgery
|
| Street address |
300 Pasteur Drive
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (2) |
| GPL11154 |
Illumina HiSeq 2000 (Homo sapiens) |
| GPL22666 |
Illumina HiSeq 2000 (Dama dama) |
|
| Samples (16)
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| GSM2389030 |
10 % Serum FD RM Cell Replicate 2 |
| GSM2389031 |
0 ng/mL BMP-2 and 0 nM Dexamethasone FD RM Cell Replicate 1 |
| GSM2389032 |
0 ng/mL BMP-2 and 0 nM Dexamethasone FD RM Cell Replicate 2 |
| GSM2389033 |
100 ng/mL BMP-2 and 100 nM Dexamethasone FD RM Cell Replicate 1 |
| GSM2389034 |
100 ng/mL BMP-2 and 100 nM Dexamethasone FD RM Cell Replicate 2 |
| GSM2389035 |
0 % Serum hMSC Replicate 1 |
| GSM2389036 |
0 % Serum hMSC Replicate 2 |
| GSM2389037 |
10 % Serum hMSC Replicate 1 |
| GSM2389038 |
10 % Serum hMSC Replicate 2 |
| GSM2389039 |
0 ng/mL BMP-2 and 0 nM Dexamethasone hMSC Replicate 1 |
| GSM2389040 |
0 ng/mL BMP-2 and 0 nM Dexamethasone hMSC Replicate 2 |
| GSM2389041 |
100 ng/mL BMP-2 and 100 nM Dexamethasone hMSC Replicate 1 |
| GSM2389042 |
100 ng/mL BMP-2 and 100 nM Dexamethasone hMSC Replicate 2 |
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| Relations |
| BioProject |
PRJNA353338 |
| SRA |
SRP093266 |
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