|
| Status |
Public on Mar 15, 2021 |
| Title |
Aortic VSMCs, G1 |
| Sample type |
SRA |
| |
|
| Source name |
Aortic Vascular Smooth Muscle Cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: NEIL3 mRNA-abrogated
cell type: Aortic Vascular Smooth Muscle Cells (primary)
|
| Treatment protocol |
NEIL3 mRNA-abrogated cells were treated with 0.5 µM NEIL3 antisense oligonucleotides for 48 hours, whereas controls were treated in parallel with a scramble version of the same antisense oligonucleotides.
|
| Growth protocol |
Cells were grown in PromoCell Growth medium and 1% penicillin Streptomycin at 37 Celsius degrees and 5% carbon dioxide.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Experimental cells cultures were lysated before and total RNA was extracted using RNeasy spin columns (Qiagen).
Library was constructed by using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® according to manufacture's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Contaminated adapter and low quality reads were trimmed with fastp (v0.20.0).
Reads were mapped to mouse cDNA (GRCh38.p13, NCBI Homo sapiens Updated Annotation Release 109.20190905) using kallisto (v0.46.0) with 100 bootstrap iterations.
sleuth (v0.30.0) was used to obtain deferentially expressed transcripts with Wald test from HDF5 file outputed by kallisto.
Genome_build: GRCh38.p13, NCBI Homo sapiens Updated Annotation Release 109.20190905
Supplementary_files_format_and_content: HDF5 (.h5) binary file which contains estimated counts, TPM, effective length of main quantification and boostraps as well as run info
normalized_kallisto_abundance_all_samples.csv.gz
|
| |
|
| Submission date |
Nov 21, 2019 |
| Last update date |
Mar 15, 2021 |
| Contact name |
Kuan Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Oslo University Hospital
|
| Department |
Research Institute of Internal Medicine
|
| Lab |
Section of Inflammatory Research
|
| Street address |
Sognsvannsveien 20
|
| City |
Oslo |
| ZIP/Postal code |
0372 |
| Country |
Norway |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE140789 |
Transcriptome profiling of primary human aortic Vascular Smooth Muscle cells abrogated of NEIL3 mRNA via antisense oligonucleotides targeting NEIL3 exon 4 |
| GSE140791 |
Role of NEIL3 in aortic Vascular Smooth Muscle cells |
|
| Relations |
| BioSample |
SAMN13343999 |
| SRA |
SRX7198370 |
