|
| Status |
Public on Dec 15, 2018 |
| Title |
pAVICs Stage 3+DMSO biological replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
porcine aortic valve interstitial cells (pAVICs)
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: aorta
cell type: aortic valve interstitial cells
calcification stages & treatment: Stage 3+DMSO
calcification stimulus: glass
|
| Treatment protocol |
Stage3+DMSO and Stage3+KPT samples received DMSO/KPT at Stage 3
|
| Growth protocol |
Cells were grown on glass for 5,8 or 12 days (depending on when the stages were observed) in DMEM media
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNAeasy kit from Qiagen
Amplified cDNA libraries suitable for sequencing were prepared from 500 nanograms (ng) of DNA-free total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.; Part # RS-122-2103).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Nod_DMSO-1
2016-12-27_Lincoln_mRNA-Seq_Anno_exons_rpkm
2016-12-27_Lincoln_mRNA-Seq_Anno_Filter_genes_rpkm
Sample name in processed data file:
SL217554
|
| Data processing |
Amplified cDNA libraries suitable for sequencing were prepared from 500 nanograms (ng) of DNA-free total RNA using the TruSeq Stranded mRNA Library Prep Kit (Illumina Inc.; Part # RS-122-2103).
Sequence alignment was performed using TopHat v2.1.0
Based on the quality results, the reads were filtered (removing sequences that did not pass Illumina’s quality filter) and trimmed
The RPKM values were filtered to retain a list of genes with a minimum of approximately 50 mapped reads in one or more samples.
Genome_build: scr3 reference genome
Supplementary_files_format_and_content: .txt files include rpkm for exons and genes for each sample
|
| |
|
| Submission date |
May 21, 2018 |
| Last update date |
Dec 15, 2018 |
| Contact name |
Punashi Dutta |
| Organization name |
Medical College of Wisconsin
|
| Department |
Cardiovascular
|
| Street address |
8701 Watertown Plank Road
|
| City |
Milwaukee |
| State/province |
WI |
| ZIP/Postal code |
53226 |
| Country |
USA |
| |
|
| Platform ID |
GPL19176 |
| Series (1) |
| GSE114726 |
RNASeq analysis of calcification stages (and KPT) in pAVICs |
|
| Relations |
| BioSample |
SAMN09233323 |
| SRA |
SRX4108630 |
