|
| Status |
Public on Nov 21, 2020 |
| Title |
HASMCs Control_1 |
| Sample type |
SRA |
| |
|
| Source name |
Human aortic smooth muscle cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primay vascular smooth muscle cells
passage: 5
treatment: PBS
|
| Treatment protocol |
At 80% confluence, cells were treated with either control (PBS) or HPbCD (10mg/mL) for 24 hours.
|
| Growth protocol |
Human aortic smooth muscle cells (HASMCs, CC-2571) were purchased from Lonza (Walkersville, MD). HASMCs were cultured in Smooth Muscle Cell Growth Medium 2 (Promo Cell, Germany) at 37°C/5% CO2 humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using RNeasy Mini Kit (74106, QIAGEN, Hilden, Germany)
RNA library preparation and sequencing were performed by the DNA sequencing core at the University of Michigan. Briefly, the RNA library was prepared with NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA) and sequenced on a NovaSeq 6000 platform (Illumina) to generate pair-end 51 bp reads according to the manufacturer’s recommendation. In total, ~250 million reads were generated with an average of 31 million paired-reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The quality control of the sequencing reads from each sample was assessed with FastQC (Babraham Bioinformatics).
The human reference cDNA sequences were downloaded from the Ensembl database (GRCh38 ftp://ftp.ensembl.org/pub/release-97/fasta/homo_sapiens/cdna/).
The reference was indexed with Salmon v 0.14.0, and gene expression quantification was performed using Salmon in its nonalignment-based mode.
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text files include count and TPM value for each sample
|
| |
|
| Submission date |
Sep 17, 2019 |
| Last update date |
Nov 23, 2020 |
| Contact name |
Haocheng Lu |
| E-mail(s) |
[email protected]
|
| Phone |
7347303682
|
| Organization name |
University of Michigan
|
| Department |
Internal Medicine
|
| Lab |
Y. Eugene Chen
|
| Street address |
2800 plymouth road
|
| City |
Ann Arbor |
| State/province |
Michigan |
| ZIP/Postal code |
48105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE137576 |
Transciptome analysis of human aortic smooth muscle cells (HASMCs) with 2-hydroxypropyl-β-cyclodextrin (HPbCD) treatment |
| GSE137577 |
Harnessing TFEB to treat abdominal aortic aneurysm |
|
| Relations |
| BioSample |
SAMN12773738 |
| SRA |
SRX6860610 |
