|
| Status |
Public on Aug 22, 2023 |
| Title |
vascular smooth muscle cells portal vein dog B |
| Sample type |
SRA |
| |
|
| Source name |
vascular smooth muscle cells portal vein
|
| Organism |
Canis lupus familiaris |
| Characteristics |
cell type: vascular smooth muscle cells
|
| 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 |
MOK5999_readCounts_raw.txt
|
| 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: raw counts
|
| |
|
| Submission date |
Apr 03, 2021 |
| Last update date |
Aug 22, 2023 |
| 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) |
| GSE171437 |
Locational memory of macrovessel vascular cells is transcriptionally imprinted |
|
| Relations |
| BioSample |
SAMN18613243 |
| SRA |
SRX10509680 |
