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| Status |
Public on Jan 12, 2021 |
| Title |
The tRNA-derived small RNAs (tsRNAs) expression profiles in human aortic vascular smooth muscle cells (HAVSMCs) |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by high throughput sequencing
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| Summary |
Purpose: Next-generation sequencing (NGS) is the main way to mine ncRNA. The purpose of this study is to screen out tRNA-derived small RNAs (tsRNAs) that are differentially expressed in proliferative and quiescent HASMCs
Methods: tsRNAs profiles of proliferative and quiescent HASMCs were generated by deep sequencing, in triplicate, using Illumina NextSeq 500. The sequence reads that passed Illumina chastity filter were used for the following analysis. Trimmed reads (with 5ʹ, 3ʹ-adaptor bases removed) were aligned to mature-tRNA and pre-tRNA reference sequences. The alignment statistical analysis was applied to retain the valid sequences for subsequent tsRNAs expression profiles and differential expression analysis.
Results: Using an optimized data analysis workflow, we mapped about 8 million sequence reads per sample to mature-tRNA and pre-tRNA sequences from GtRNAdb and identified 3,891 tsRNAs in the proliferative and quiescent HASMCs. According to the standardized TPM, 887 up-regulated and 951 down-regulated tsRNAs were found in the proliferative HASMCs (fold change > 2, P < 0.05).
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| Overall design |
HASMCs were cultured using Smooth Muscle Cell Medium containing 2% fetal bovine serum, 1% 100 × Smooth Muscle Cell Growth Supplement and 1% 100 × Penicillin/Streptomycin Solution at 37°C in a humidified chamber with 5% CO2 and 95% O2. Quiescent HASMCs were induced by FBS starvation for 24 hours.
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| Contributor(s) |
Sun S, Zhao J, Li B |
| Citation(s) |
35705912 |
| |
| Submission date |
Jan 11, 2021 |
| Last update date |
Jun 27, 2022 |
| Contact name |
shaoguang sun |
| E-mail(s) |
sunshaog@hebmu.edu.cn
|
| Phone |
8631186265639
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| Organization name |
Hebei medical university
|
| Department |
biochemistry and molecular biology
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| Street address |
zhong shan dong lu 361
|
| City |
shi jia zhuang |
| State/province |
Hebei |
| ZIP/Postal code |
050017 |
| Country |
China |
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| Platforms (1) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA691152 |
| SRA |
SRP301214 |
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