|
| Status |
Public on Feb 07, 2022 |
| Title |
HUVEC_NC_3 |
| Sample type |
SRA |
| |
|
| Source name |
Primary human umbilical vein cells (HUVECS
|
| Organism |
Homo sapiens |
| Characteristics |
material: Cell culture
cell type: Primary human umbilical vein cells (HUVECS
transfection: transfection with negative controle
stimulation: TNF stimulation (25 ng/ml) for 6h
|
| Treatment protocol |
18 hours after transfection with NEON transfection system cells were TNF stimulation (25 ng/ml) for additional 6 hours
|
| Growth protocol |
Primary Human Umbilical Vein Endothelial Cells (HUVEC) were isolated from umbilical cords of healthy neonates. HUVEC were isolated from umbilical vein vascular wall by collagenase A (Roche) treatment and cultured in Endothelial Cell Basal Medium (ECGM; PromoCell) with SupplementMix (PromoCell), 10% FCS (Biochrom AG) and 1% Penicillin/Streptomycin (Pen/Strep, Gibco). Cells of one single cord at passage 2-4 were used for each of the independent experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using miRNeasy Mini kit (Qiagen)and analyzed by IMGM Laboratories GmbH (Martinsried, Germany). Quality control for all total RNA samples was done on the 2100 Bioanalyzer (Agilent Technologies) using RNA 6000 Nano LabChip Kits (Agilent Technologies).
Library preparation was performed with the TruSeq Stranded mRNA HT technology (Illumina), according to the manufacturer's protocol, including fragmentation, a poly-T oligo pulldown and sequencing adapter ligation. RNA sequencing was performed on the Illumina NextSeq 500 next generation sequencing system and its high output mode with 1 x 75 bp single-end read chemistry with >10 million reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The RNA-Seq analysis was performed with the CLC Genomics Workbench “RNA-Seq analysis” tool.
The human reference genome (GRCh38.p7) was downloaded from NCBI and used as reference sequence.
For mapping purposes of the generated *.fastq files, reads were mapped according to their similarity to the reference sequences. The following mapping parameters were applied: Mismatch cost: 2; Insertion/Deletion cost: 3; Length fraction: 0.8; Similarity; fraction: 0.8; Maximum number of hits per read: 5
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated occording to the method described by Mortazavi et al. Nat Methods. Juli 2008;5(7):621–8.
Genome_build: GRCh38.p7
Supplementary_files_format_and_content: tab-delimited text files include TPM and RPKM values for each sample
|
| |
|
| Submission date |
Feb 04, 2022 |
| Last update date |
Feb 08, 2022 |
| Contact name |
Martin Bernhard Mueller |
| E-mail(s) |
Martin_Bernhard.Mueller@med.uni-muenchen.de
|
| Organization name |
University Hospital, Ludwig-Maximilians-University Munich (LMU)
|
| Department |
Department of Anaesthesiology
|
| Lab |
Walter Brendel Center of Experimental Medicine (WBex)
|
| Street address |
Marchioninistrasse 15
|
| City |
Munich |
| ZIP/Postal code |
81377 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE196161 |
RNA-Seq of inflammatory stimulated HUVECs transfected with microRNA-125a-5p or negative control. |
|
| Relations |
| SRA |
SRX13242179 |
| BioSample |
SAMN23470209 |
