|
Status |
Public on Dec 01, 2021 |
Title |
TIME42 |
Sample type |
SRA |
|
|
Source name |
TIME
|
Organism |
Homo sapiens |
Characteristics |
cell type: endothelial cell supplement: AA 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.
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|
|
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
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|
|
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 |
SAMN13551962 |
SRA |
SRX7360000 |