|
| Status |
Public on Sep 11, 2019 |
| Title |
PreTAVR_E |
| Sample type |
SRA |
| |
|
| Source name |
Aortic valve leaflets
|
| Organism |
Sus scrofa |
| Characteristics |
cell type: Valvular Interstitial Cell
passages: P1
animal age: 5-6 months
|
| Treatment protocol |
Pre-TAVR and post-TAVR serum from 8 patients (4 male and 4 female) were tested in this experiment, resulting in 16 total samples.
|
| Growth protocol |
Male and female porcine VICs were isolated, seeded on PEG-norbornene hydrogels (elastic modulus ~5.8 kPa), and cultured in Media 199 (Life Technologies) supplemented with 1% human serum, 50 U/mL penicillin, 50 μg/mL streptomycin, and 1 μg/mL amphotericin B for 48 hours.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
mRNA was isolated using an RNeasy Micro Kit (Qiagen) according to the manufacturer’s protocol.
RNA quality was assessed using an Agilent 2100 Bioanalyzer prior to library construction. RNA libraries were constructed using the mRNA KAPA Hyperprep kit (Kapa Biosystems).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Pre-TAVR serum treatment from human patient E
ProcessedDataFile.xlsx
|
| Data processing |
Samples were sequenced on the NextSeq 500 (Illumina) using a high-output 75-cycle kit (single read, 1x75 bp).
Read quality, in fastq format, was evaluated using FastQC (V0.11.5)
Adapter sequences were removed from fastq files using Trimmomatic (V0.36)
Trimmed fastq read files were aligned to the sus scrofa genome (GCF_000003025.6_Sscrofa11.1_genomic.gff, obtained from NCBI) using the hierarchical indexing for spliced alignment of transcripts software known as HISAT2 (V2.1.0)
After converting aligned read sam files to bam files using Samtools (V1.3.1), transcript alignment was performed using the Rsubread and featureCounts
Counts were obtained using Rsubread (V1.30.9)
Genome_build: SusScrofa 11.1
Supplementary_files_format_and_content: The processed data file (ProcessedDataFile.xlsx) contains CPM values.
|
| |
|
| Submission date |
Jun 28, 2019 |
| Last update date |
Sep 11, 2019 |
| Contact name |
Kristi Anseth |
| Organization name |
University of Colorado - Boulder
|
| Street address |
3415 Colorado Ave, 596 UCB
|
| City |
Boulder |
| State/province |
CO- COLORADO |
| ZIP/Postal code |
80309 |
| Country |
USA |
| |
|
| Platform ID |
GPL20983 |
| Series (1) |
| GSE133529 |
Transcatheter aortic valve replacements alter circulating serum factors to mediate myofibroblast deactivation |
|
| Relations |
| BioSample |
SAMN12163247 |
| SRA |
SRX6384214 |
