|
| Status |
Public on Nov 22, 2023 |
| Title |
VSMCs Pi-3 |
| Sample type |
SRA |
| |
|
| Source name |
thoracic aorta
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: thoracic aorta
cell type: Primary thoracic aortic smooth muscle cells
genotype: WT
treatment: Osteogenic differentiation
|
| Treatment protocol |
Osteogenic differentiation was induced by treatment with osteogenic media (OM) (10mM β-GP plus 3.5mM CaCl2) with or without empagliflozin (1uM) for 5days.
|
| Growth protocol |
VSMCs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin (P/S) in humidified atmosphere with 5% CO2 at 37℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol reagent (Invitrogen, Waltham, MA) and 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq prepared using NEBNext® UltraTM RNA Library Prep Kit ( E7530L, NEB, USA) following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Pi-3
|
| Data processing |
Raw data (raw reads) of fastq format were firstly processed through fastp.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: Reference genome and gene annotation files were downloaded from genome website. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. W
Supplementary files format and content: RSEM was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Supplementary files format and content: Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package, include Genes with an adjusted P-value <0.05 for each sample.
|
| |
|
| Submission date |
Sep 21, 2023 |
| Last update date |
Nov 22, 2023 |
| Contact name |
Junping Li |
| E-mail(s) |
lijp58@mail2.sysu.edu.cn
|
| Organization name |
Sun Yat-sen Memorial Hospital, Sun Yat-sen University
|
| Street address |
107 Yanjiang West Road, Yuexiu District, Guangzhou, Guangdong Province, China
|
| City |
Guangzhou |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE243752 |
Empagliflozin alleviates atherosclerotic calcification by inhibiting osteogenic differentiation of vascular smooth muscle cells |
|
| Relations |
| BioSample |
SAMN37502869 |
| SRA |
SRX21855142 |
