|
| Status |
Public on Jun 25, 2019 |
| Title |
RNAseq_HCAEC_0h_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Endothelial Cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human Coronary Artery Endothelial Cells
passages: passages 7 to 9
tnf-alpha treatment: 0h
|
| Treatment protocol |
Endothelial cells were treated with TNF-alpha prepared in culture media at 10 ng/mL for 4h and 24h periods
|
| Growth protocol |
Immortalized human aortic endothelial cells (teloHAEC) were grown in vascular cell basal media supplemented with endothelial cell growth kit-VEGF, 200 U/mL penicillin and 200 μg/mL of streptomycin. Primary human coronary artery endothelial cells (HCAEC) from a single male donor were grown in EGM-2MV supplemented with 200 U/mL penicillin and 200 μg/mL of streptomycin. TeloHAEC and HCAEC (below 3 passages) were maintained under a 5% CO2 atmosphere at 37°C. Endothelial cells were seeded at 2x10^5 cells per well in 6-well plates, grown for 3 days (refreshed media at day 2) until reaching 95-100% confluency and subjected to TNF-alpha treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using RNeasy Plus Mini kit (Qiagen)
NEBNext mRNA Library Prep Reagent Set for Illumina
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNAseq_HCAEC_abundance.txt
|
| Data processing |
Reads were mapped to hg19 using hisat2 (http://ccb.jhu.edu/software/hisat2/index.shtml).
Samtools was used to sort the reads and convert to the BAM format.
Transcripts were first identified for each sample, and then pooled together using stringtie (http://ccb.jhu.edu/software/stringtie/index.shtml)
Transcript abundance was estimated by stringtie and a fragments per kilobase of transcript per million (FPKM) count table was generated
Differential analysis of gene expression was performed using DESeq2 (Love et al. 2014). All possible comparisons for NT, TNFα 4 hours and 24 hours treatments were performed using the analysis of deviance function with default parameters. Genes with a false discovery rate (FDR, Benjamini & Hochberg correction) ≤0.001 and fold-change ≥2 or ≤-2 were considered differentially expressed.
Corresponding biological replicates output were merged using UCSC BigWig and BigBed tools (Kent et al. 2010)
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files correspond to coverage per bp for merged biological replicates for each condition; abundance measurements corresponds to transcripts FPKM table for each cell line
|
| |
|
| Submission date |
Feb 06, 2019 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Guillaume Lettre |
| E-mail(s) |
[email protected]
|
| Organization name |
Montreal Heart Institute
|
| Street address |
5000 Rue Bélanger
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H1T 1C8 |
| Country |
Canada |
| |
|
| Platform ID |
GPL20301 |
| Series (2) |
| GSE126198 |
Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene (RNAseq) |
| GSE126200 |
Integrative vascular endothelial cell genomics identify AIDA as a coronary artery disease candidate gene |
|
| Relations |
| BioSample |
SAMN10882012 |
| SRA |
SRX5345168 |
