|
| Status |
Public on May 01, 2024 |
| Title |
HUVEC, TNFa3 |
| Sample type |
SRA |
| |
|
| Source name |
HUVEC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUVEC
cell type: endothelial cell
treatment: TNFa
|
| Treatment protocol |
HUVEC cells were cultured at 2X10(5)/well in the 6-well plate. The next day, the cell medium was replaced with 10 ng/ml TNFa, 10 ng/ml IL-4, 50 ng/ml IFNg, or control (EGM-2 medium only) and cultured 2 days. RNA was isolated and used for the library generation.
|
| Growth protocol |
HUVEC was maintained with EGM-2 medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted by TRIzol
PolyA RNA was isolated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and barcoded libraries were made using the NEBNext® Ultra II™ Directional RNA Library Prep Kit for Illumina®(NEB, Ipswich MA).
Libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2 kit (Illumina Inc., San Diego CA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
06_B3TNFa
|
| Data processing |
Read data was processed in BaseSpace (basespace.illumina.com). Reads were aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Assembly: Reads were aligned to Homo sapiens genome (hg19) using STAR aligner (https://code.google.com/p/rna-star/) with default settings.
Supplementary files format and content: fpkm
|
| |
|
| Submission date |
Feb 02, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
JUNKO SAWADA |
| E-mail(s) |
jsawada1@jhmi.edu
|
| Organization name |
Johns Hopkins All Children's Hispital
|
| Street address |
600 5th Street South
|
| City |
St. Petersburg |
| ZIP/Postal code |
33701 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE254958 |
The gene expression of HUVEC in response to the cytokine stimulations |
|
| Relations |
| BioSample |
SAMN39750107 |
| SRA |
SRX23510055 |
