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Sample GSM4221355 Query DataSets for GSM4221355
Status Public on Mar 05, 2020
Title 03_Ctrl
Sample type SRA
 
Source name adenovirus 80 MOI expressing empty vector for 48h
Organism Homo sapiens
Characteristics cell type: Pluripotent stem-cell derived endothelial cells
sample label: 103
treatment: Ctrl
replicate: 3
Treatment protocol Cells were treated with adenovirus for 48h at MOI 20 or 80.
Growth protocol Expansion medium consisting of StemPro with 50 ng/mL of VEGFA was used for the first cell division, after which cells were cultured using VascuLife VEGF Endothelial Medium Complete Kit (LifeLine Cell Technology). The final composition of supplements added to the media was as follows: 10% FBS, 4 mM L-glutamine, 0.75 U/mL heparin sulfate, 5 ng/mL FGF-2, 5 ng/mL EGF, 5 ng/mL VEGFA, 15 ng/mL IGF1, 1 µg/mL hydrocortizone hemisuccinate, and 50 µg/mL Ascorbic acid. SB431542 (10 µM) was supplemented to the media.
Extracted molecule total RNA
Extraction protocol Cultured ECs were lysed using 350 μL RLT lysis buffer (Qiagen) with β-mercaptoethanol (1%) and subsequently vortexed for 1 min at room temperature before snap freezing. RNA was isolated from cell lysates using an automated Maxwell Total RNA purification kit (Promega) with DNAse I digestion.
Total RNA was subjected to oligo (dT) capture and enrichment, and the resulting mRNA fraction was used to construct cDNA libraries. Sequencing was performed on an Illumina HiSeq 4000 platform using the standard protocol (TruSeq Stranded Total RNA Library, Illumina) that generates approximately 30 million reads of 50 base pairs per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Description Treatment with adenovirus 80 MOI expressing empty vector for 48h (control)
Data processing Basecalling and sample de-multiplexing was performed with CASAVA-1.8.4 and default parameters
Reads were quality check with fastqc v0.11.5 default parameters
Reads for each sample/replicate were mapped against the human genome assembly using STAR read aligner v2.5.2a
RefSeq annotated genes were quantified with samtools v1.5 and in-house scripts
Genome_build: hg38
Supplementary_files_format_and_content: Read counts per gene
 
Submission date Dec 16, 2019
Last update date Mar 05, 2020
Contact name Roland Schmucki
E-mail(s) roland.schmucki@roche.com
Organization name F. Hoffmann - La Roche AG
Street address Grenzacherstrase
City Basel
ZIP/Postal code 4058
Country Switzerland
 
Platform ID GPL20301
Series (2)
GSE142131 Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector of different combination of transcription factors
GSE142132 Genome wide RNA-sequencing of human pluripotent stem-cell derived endothelial cells 48h after transduction with adenoviruses expressing either empty vector, single or multiple transcription factors
Relations
BioSample SAMN13577657
SRA SRX7388530

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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