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Sample GSM1537565 Query DataSets for GSM1537565
Status Public on Jan 16, 2015
Title Mouse siRNA control rep2
Sample type SRA
 
Source name Endothelial
Organism Mus musculus
Characteristics cell line: C166
treatment: siRNA control
tissue: Yolk sac
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_C166.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 GPL17021
Series (1)
GSE62974 RNA sequencing (RNA-SEQ) of EPAS1 knockdown by siRNA in endothelial cells
Relations
BioSample SAMN03161488
SRA SRX750945

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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