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Sample GSM8229229 Query DataSets for GSM8229229
Status Public on May 01, 2024
Title TNFa1
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 SAMN41074279
SRA SRX24360434

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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