|
| Status |
Public on Jan 24, 2018 |
| Title |
hyp_24h_n1_1 |
| Sample type |
SRA |
| |
|
| Source name |
Human umbilical vein endothelial cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Endothelial cells
passage: Passage 2
treatment: Hypoxia 0.2% O2, 5% CO2 humidified atmosphere
|
| Treatment protocol |
Hypoxia (0.2% O2) was induced in a humidified atmosphere. Hypoxic pO2 levels were verified by measuring VEGFA induction by RT-qPCR and pO2 levels with a hypoxia sensing probe from Oxford Optronix (Oxford, UK). RNA was isolated and processed for RNA deep sequencing.
|
| Growth protocol |
Pooled human umbilical vein endothelial cells (Lonza) were cultured as recommended by the manufacturer. Cells were kept at 5% CO2, 20% O2, 37°C and humidified atmosphere. Endothelial cell were cultured in endothelial basal medium containing EGM SingleQuots (Lonza) and 10% fetal calf serum (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA deep sequencing was performed by analyzing ribosomal depleted total RNA from human umbilical vein endothelial cells. RNA was isolated using a RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions including DNA digestion.
RNA was fragmented and primed for cDNA synthesis. Libraries were created using a NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina as recommended by the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Hypoxic conditions
|
| Data processing |
Reads were mapped with Tophat default parameters to GRCH37. Afterwards, FPKM values where determined by Cuffdiff.
Genome_build: GRCH37
Supplementary_files_format_and_content: Tab delimited text file wich includes FPKM values for each sample
|
| |
|
| Submission date |
Nov 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Philipp Neumann |
| E-mail(s) |
der.philipp.neumann@gmail.com
|
| Organization name |
Institute for Cardiovascular Regeneration
|
| Street address |
Theodor-Stern-Kai 7
|
| City |
Frankfurt am Main |
| State/province |
Hessen |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE107029 |
Total RNA deep sequencing (ribosomal depleted) of human umbilical vein endothelial cells exposed to hypoxia (0.2%) for 12h and 24h or kept under normoxic conditions. |
| GSE107033 |
Endothelial gene expression analysis |
|
| Relations |
| BioSample |
SAMN08035736 |
| SRA |
SRX3401583 |
