|
| Status |
Public on Aug 03, 2018 |
| Title |
vena_cava3_vSMC |
| Sample type |
SRA |
| |
|
| Source name |
vena_cava_vSMC
|
| Organism |
Canis lupus familiaris |
| Characteristics |
tissue: vena_cava
cell type: vascular smooth muscle cell
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cells were trypsinized and stored in RLT. Total RNA was isolated using a RNeasy Mini Kit (Qiagen).
Sequencing libraries were prepared using the Rapid Directional RNA-Seq Kit (NEXTflex)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
readCounts_raw.txt
processed data file column: SMCvcISO5
|
| Data processing |
RNA-seq reads were aligned to the reference genome using STAR version 2.4.2a
Read groups were added to the BAM files with Picard's AddOrReplaceReadGroups
The BAM files are sorted with Sambamba v0.4.5 and transcript abundances were quantified with HTSeq-count version 0.6.1p1, using the union mode.
Genome_build: canfam3.1
Supplementary_files_format_and_content: readCounts_raw.txt
|
| |
|
| Submission date |
Aug 02, 2018 |
| Last update date |
Aug 03, 2018 |
| Contact name |
Frank van Steenbeek |
| E-mail(s) |
f.g.vansteenbeek@uu.nl
|
| Phone |
0302532848
|
| Organization name |
Utrecht University
|
| Street address |
Yalelaan 104
|
| City |
Utrecht |
| State/province |
Select State/Province |
| ZIP/Postal code |
3584 CM |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL21400 |
| Series (1) |
| GSE118029 |
Characterization of endothelial and smooth muscle cells from different canine vessels |
|
| Relations |
| BioSample |
SAMN09760109 |
| SRA |
SRX4501266 |
