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| Status |
Public on Mar 05, 2020 |
| Title |
Next Generation Sequencing Facilitates Quantitative Analysis of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl Incisor Transcriptomes |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived incisor transcriptome profiling (RNA-seq) between Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice to identify the potential target of Runx2.
Methods: Incisor mRNA profiles from one week after induction of one-month-old Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.
Results: Using an optimized data analysis workflow, we mapped about 68 million sequence reads per sample to the mouse genome ( mm10) and identified 80,214 transcripts in th incisors of Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice with Partek E/M workflow. Five hundred and eleven differentially regulated genes were identified (＞2-fold, p＜0.05), of which 299 were upregulated and 212 were downregulated.
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| Overall design |
Incisor mRNA profiles from one week after induction of one-month-old Runx2fl/fl and Gli1-CreERT2;Runx2fl/fl mice were generated by deep sequencing, in triplicate, using Illumina NextSeq500.
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| Contributor(s) |
Chen S, Chai Y |
| Citation(s) |
32783935 |
| |
| Submission date |
Mar 04, 2020 |
| Last update date |
Sep 08, 2020 |
| Contact name |
Shuo Chen |
| E-mail(s) |
sc_398@usc.edu
|
| Phone |
3233184193
|
| Organization name |
Center for Craniofacial Molecular Biology, University of Southern California
|
| Street address |
2250 Alcazar Street, Clinical Science Annex, Room 103, CLINICAL SCIENCE ANNEX ROOM 103
|
| City |
Los Angeles |
| State/province |
California |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE154158 |
The Gene expression profiling by high throughput sequencing in adult mouse incisor |
|
| Relations |
| BioProject |
PRJNA610172 |
| SRA |
SRP251495 |
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