|
| Status |
Public on Oct 15, 2021 |
| Title |
Myocd-LSD1_RNA-4 |
| Sample type |
SRA |
| |
|
| Source name |
Aortic SMC
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: Myocd-LSD1
cell type: Aortic SMC
treatment: untreated
|
| Treatment protocol |
SMC were starved in ISFM for 48 hours and then treated with human recombinant PDGF-BB constituted in 10 mM Acetic Acid at 30 ng/ml for treatment in ISFM for 24 hours.
|
| Growth protocol |
Cell lines were cultured in growth medium (DMEM/F12, Gibco) supplemented with FBS (10%, Corning), L-glutamine (1.6 mM, Gibco) and penicillin-streptomcyin (100 U/ml, Gibco). Before harvesting for RNAseq, cells were starved in a serum-free, insulin-free medium (ISFM) for 72 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from cells using Rneasy Mini Kit (Qiagen) following manufacture's protocol. Genomic DNA was removed using Dnase I (Qiagen).
RNA library was prepared by TruSeq Stranded mRNA (Poly A+) according ot manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RNAseq_Expression Browser_TPM.xlsx
|
| Data processing |
The 75 bp paired-end reads were mapped to Rattus Norvegicus reference genome Rn6 and gene ID were mapped to Rattus Norvegicus ensembl_v91 using default setting by CLC Genomic Workbench (Qiagen).
All mapped reads were normalized by Trimmed Mean of M values (TMM normalization) for differential gene expression analysis in CLC Genomic Workbench (Qiagen)
Genome_build: Rn6
Supplementary_files_format_and_content: Matrix table of normalized gene counts (TPM) for each sample
|
| |
|
| Submission date |
Jun 30, 2021 |
| Last update date |
Oct 15, 2021 |
| Contact name |
Delphine Gomez |
| E-mail(s) |
gomezd@pitt.edu
|
| Phone |
412-383-3269
|
| Organization name |
University of Pittsburgh
|
| Department |
Medicine, division of Cardiology
|
| Lab |
Delphine Gomez Lab
|
| Street address |
200 Lothrop Street
|
| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15261 |
| Country |
USA |
| |
|
| Platform ID |
GPL20084 |
| Series (2) |
| GSE179215 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis [RNAseq] |
| GSE179220 |
H3K4 di-methylation controls smooth muscle cell lineage identity and vascular homeostasis |
|
| Relations |
| BioSample |
SAMN19971610 |
| SRA |
SRX11318178 |
