|
| Status |
Public on Jan 16, 2015 |
| Title |
Human endothelial siRNA control rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Endothelial
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: HUVEC
treatment: siRNA control
tissue: umbilical vein/vascular endothelium
|
| Growth protocol |
The cell lines of HUVEC (Lonza, MD, USA) and C166 (American Type Culture Collection, VA, USA) were cultured in the appropriate media at 37°C with 5% CO2. The cells were transfected with EPAS1 siRNA and non-targeting negative control siRNA (Life Technologies, CA, USA) using Lipofectamine RNAiMAX as recommended transfection protocols by the manufacturer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After the treatments with 5nM Silencer® Select siRNA (s4700 for EPAS1, s65525 for Epas1; Life Technologies, USA) for 48 hours, the total RNA was purified with RNeasy Mini Kit (QIAGEN, Germany). The efficiencies of knocked down the EPAS1 expression were assessed by qPCR with 1.4% for HUVEC, 3.2% for C166.
Approximately 250 ng of total RNA per sample were used for library construction by the TruSeq RNA Sample Prep Kit (Illumina) and sequenced using the Illumina HiSeq 2500 instrument with 100nt single read setting according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
FPKM_HUVEC.txt
|
| Data processing |
Sequence reads are mapped and aligned to human (hg19) and mouse (mm10) genome assembly for HUVEC and C166, respectively, and then quantified in terms of FPKM using Cufflinks.
Genome_build: hg19 for HUVEC and mm10 for C166
Supplementary_files_format_and_content: tab-delimited text file including FPKM values of each gene for each Sample
|
| |
|
| Submission date |
Nov 04, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Seungyeul Yoo |
| Organization name |
Icahn School of Medicine at Mount Sinai
|
| Department |
Genetics and Genomic Sciences
|
| Lab |
Integrative Network Biology Group
|
| Street address |
1425 Madison Avenue
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10029 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE62974 |
RNA sequencing (RNA-SEQ) of EPAS1 knockdown by siRNA in endothelial cells |
|
| Relations |
| BioSample |
SAMN03161479 |
| SRA |
SRX750953 |
