|
| Status |
Public on Jan 19, 2022 |
| Title |
Hypoxia_DMSO_HUVEC_2 [Hyp-DMSO_2] |
| Sample type |
SRA |
| |
|
| Source name |
Hypoxia_DMSO_HUVEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: human umbilical vein endothelial cells (HUVEC)
treatment: 16h (1% O2) with DMSO
|
| Treatment protocol |
Hypoxia was performed for 16h (1% O2) with DMSO or Acriflavine (10µM) treatment.
|
| Growth protocol |
Culturing of pooled human umbilical vein endothelial cells (HUVEC) purchased from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042, Heidelberg, Germany) was performed at 37°C with 5% CO2. Dishes were coated with gelatin (Sigma-Aldrich, G1890-500G) prior to culturing. Endothelial growth medium (EGM) was prepared by supplementing endothelial basal medium (EBM) with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (15140-122, Gibco/ Lifetechnologies, USA). Biological replicates comprised at least three different batches from passage 3. For hypoxia treatment, cells were incubated for 16h in a SciTive Workstation (Baker Ruskinn, Leeds, UK) at 1% O2 and 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA Isolation was performed using the RNA Mini Kit (Bio&Sell).
1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) using manufactures protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
E21_3141_Lib_Leisegang_ML1529-2_Probe_10
|
| Data processing |
The resulting raw reads were assessed for quality, adapter content and duplication rates with FastQC.
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (ensemble release 104) using STAR 2.7.9a with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 2.0.2 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data based on Ensembl gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library size normalized counts
|
| |
|
| Submission date |
Oct 21, 2021 |
| Last update date |
Jan 19, 2022 |
| Contact name |
Stefan Günther |
| E-mail(s) |
stefan.guenther@mpi-bn.mpg.de
|
| Organization name |
MPI for heart and lung research
|
| Street address |
ludwigtr. 43
|
| City |
bad nauheim |
| ZIP/Postal code |
61231 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE186297 |
Effects of DNA topoisomerase inhibitor acriflavine on endothelial gene expression under hypoxic conditions |
|
| Relations |
| BioSample |
SAMN22456151 |
| SRA |
SRX12721054 |
