|
| Status |
Public on Oct 01, 2022 |
| Title |
Silenz_II_Exp_R1 |
| Sample type |
SRA |
| |
|
| Source name |
Ctrl- mouse endothelial cells
|
| Organism |
Mus musculus |
| Characteristics |
condition: Ctrl-Silenced
cell type: Immortalised aortic endothelial cells
|
| Treatment protocol |
Stealth RNAi duplexes designed against mouse Pdcd10 (Thermo Fisher Scientific, USA, PDCD10HSS174173; PDCD10HSS117454; PDCD10HSS117455) or stealth RNAi negative control (Thermo Fisher Scientific, USA, cat#12935115) were transfected in ECs cells (siPdcd10-ECs and Ctrl-ECs respectively) using Lipofectamine RNAiMAX (Thermo Fisher Scientific, USA) according to the manufacturer's protocol.
|
| Growth protocol |
Immortalised mouse endothelial cells (ECs) were cultured in D-MEM with Glutamax supplemented with 20% FBS and 1% penicillin (100 U/ml) and streptomycin (100 μg/ml) (Thermo Fisher Scientific, USA) and grown in a 5% CO2 incubator at 37° C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using mini RNase kit reagent (Qiagen, Tübingen, Germany).
Poly-A enriched library were generated with the TruSeq RNA-Seq Library Preparation Kit v2 (#RS-122-2001, Illumina) according to the manufacturer’s instructions. Library quality control was performed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Indexed libraries were sequenced at CRS4 Next Generation Sequencing facility with the HiSeq 3000 instrument to generate ~40M 50bp single-end reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Silenz_II_Exp_R1
|
| Data processing |
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk 37.31
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with RSEM 1.3.0
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files including raw counts
|
| |
|
| Submission date |
Oct 25, 2021 |
| Last update date |
Oct 02, 2022 |
| Contact name |
Lucio Di Filippo |
| E-mail(s) |
difilippolucio@gmail.com
|
| Organization name |
ngd
|
| Street address |
Via Campi Flegrei 34
|
| City |
Pozzuoli |
| State/province |
Napoli |
| ZIP/Postal code |
80078 |
| Country |
Italy |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE186523 |
Transcriptome analysis revealed altered response to hypoxia, inflammation and immune regulation in Pdcd10-depleted endothelial cells |
|
| Relations |
| BioSample |
SAMN22561470 |
| SRA |
SRX12764315 |
