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Sample GSM8033096 Query DataSets for GSM8033096
Status Public on May 10, 2024
Title VSMC, WT, Day1,rep3
Sample type SRA
 
Source name Aorta
Organism Mus musculus
Characteristics tissue: Aorta
cell line: VSMC
cell type: Primary
genotype: WT
treatment: none
Treatment protocol Cells at approximately 80 % confluence were cultured in DMEM/F12 medium containing 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin, and 10 mM β-GP.
Growth protocol Cells were cultured in DMEM/F12 medium containing 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin, and 10 mM β-GP.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from the cultured cell samples using TRIzol Reagent. RNA quality and quantity were measured using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations, and index codes were Sequencing libraries were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s recommendations, and index codes were added to attribute sequences to each sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing To select complementary DNA fragments of preferentially 250 to 300 base pairs (bp) in length, the library fragments were purified with an AMPure XP system
USER Enzyme (NEB) was used with size-selected fragments and polymerase chain reaction (PCR) products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system
The clustering of the index-coded samples was performed on the cBot Cluster Generation System using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions
After cluster generation, the library preparations were sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes counts for each sample
Supplementary files format and content: tab-delimited text file include RPKM values for each sample
 
Submission date Jan 24, 2024
Last update date May 10, 2024
Contact name Wenqi Ma
E-mail(s) wenqiM@hotmail.com
Phone +8615905172287
Organization name Shanghai Jiaotong University
Street address 227 Chongqing South Road, Huangpu District, Shanghai, China
City Shanghai
State/province Shanghai
ZIP/Postal code 20025
Country China
 
Platform ID GPL24247
Series (2)
GSE254077 Effect of depletion of NR4A3 on vascular calcification [RNA-seq]
GSE254078 NR4A3耗尽对血管钙化的影响
Relations
BioSample SAMN39595387
SRA SRX23376945

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

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