|
| Status |
Public on Dec 01, 2021 |
| Title |
TIME56 |
| Sample type |
SRA |
| |
|
| Source name |
TIME
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial cell
supplement: DHA supplemented
stimulation: cytokine
|
| Treatment protocol |
The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling 144 h. Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml.
|
| Growth protocol |
Cells were cultured according to ATCC recommendations.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared by Novogene according to Illumina's instructions accompanying the NEB Next Ultra RNA Library Prep Kit.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Low quality read ends as well as remaining parts of sequencing adapters were clipped off using Cutadapt (v 1.14) with parameters -q 20 -O 7 -m 20
Trimmed reads were mapped against the human genome (hg38 UCSC) using HiSat2 (v 2.1.0) with parameters -p 6 --dta --strandness RF -k 5
secondary alignments were filtered out using samtools (v 1.5)
Mapped reads were summarized using featureCounts (v 1.5.3) with parameters -p -s 2 -M -t exon -g gene_id and Ensembl gene annotations (GRCh 38.89)
Differential gene expression was assessed using R/edgeR (v 3.18.1) using TMM normalization
Genome_build: hg38
Supplementary_files_format_and_content: tab-separated text file containing raw counts for each sample
|
| |
|
| Submission date |
Dec 12, 2019 |
| Last update date |
Dec 01, 2021 |
| Contact name |
Julia Schumann |
| E-mail(s) |
julia.schumann@uk-halle.de
|
| Organization name |
University Medicine Halle (Saale)
|
| Street address |
Franzosenweg 1a
|
| City |
Halle (Saale) |
| ZIP/Postal code |
06112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE141957 |
mRNA expression profiles (transcriptome) of human endothelial cells (cell line: TIME) |
| GSE142090 |
mRNA expression profiles (transcriptome) of TIME and RAW264.7 |
|
| Relations |
| BioSample |
SAMN13551958 |
| SRA |
SRX7360004 |
