|
| Status |
Public on May 01, 2024 |
| Title |
TNFa2 |
| Sample type |
SRA |
| |
|
| Source name |
endothelium
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: endothelium
cell type: Human Umbilical Vein Endothelial Cells
genotype: WT
treatment: Ad-NC+TNFa
|
| Treatment protocol |
HUVECs were treated with AdNC or Ad-IGFBP6 for 24 hours and with or without TNF-α (10ng/ml) for 6 hours.
|
| Growth protocol |
Cells were cultured in M200 media supplemented with 5% FBS and 1X ECGS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was harvested using RNAeasy Mini Kit from Qiagen.
RNA libraries were prepared for sequencing using rRNA Removal Library Construction Protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Data processing |
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format.
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Bowtie2 (v2.2.5) was applied to align the clean reads to the gene set, a database built by BGI (Beijing Genomic Institute in ShenZhen), in which known and novel, coding and noncoding transcripts were included
Expression level of gene was calculated by RSEM(v1.2.12).
Assembly: GRCh38.p12
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Apr 24, 2024 |
| Last update date |
May 01, 2024 |
| Contact name |
Meiming Su |
| E-mail(s) |
Sumeiming@mail.ustc.edu.cn
|
| Organization name |
USTC
|
| Street address |
Huangshan Road
|
| City |
Hefei |
| ZIP/Postal code |
230026 |
| Country |
China |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE265787 |
Endothelial IGFBP6 Suppresses Vascular Inflammation and Atherosclerosis |
|
| Relations |
| BioSample |
SAMN41074278 |
| SRA |
SRX24360435 |
