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Sample GSM4217057 Query DataSets for GSM4217057
Status Public on Dec 01, 2021
Title TIME9
Sample type SRA
 
Source name TIME
Organism Homo sapiens
Characteristics cell type: endothelial cell
supplement: unsupplemented
stimulation: unstimulated
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 SAMN13551973
SRA SRX7359989

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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