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Sample GSM8033086 Query DataSets for GSM8033086
Status Public on May 10, 2024
Title VSMC, WT, NR4A3 CUT&Tag, REP2
Sample type SRA
 
Source name Aorta
Organism Mus musculus
Characteristics tissue: Aorta
cell line: VCMC
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 genomic DNA
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
Libraries were sequenced on Illumina Nova-PE150, and 150-bp paired-end reads were generated
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NovaSeq 6000
 
Data processing *library strategy: CUT&Tag
All reads produced by CUT&Tag of NR4A3 and H3K18la were aligned to the Mouse reference genome (UCSC, mm10 assembly) using Bowtie2 with options: –local– very-sensitive-local–no-unal–no-mixed–no-discordant–phred33 -I 10 -X 700.
Sequence tags were aligned to the genome and then subsequently analyzed by MACS2 (version 2.2.7.1) to detect genomic regions enriched for multiple overlapping DNA fragments (peaks) that we considered to be putative binding sites.
We considered differential peaks with FDR lower than 5 % as statistically significant.
Visualization of peak distribution along genomic regions of interested genes was performed with IGV.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts for each sample
Supplementary files format and content: bigwig, narrowpeak
 
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)
GSE254076 Effect of depletion of NR4A3 on vascular calcification [CUT&Tag_NR4A3]
GSE254078 NR4A3耗尽对血管钙化的影响
Relations
BioSample SAMN39594731
SRA SRX23376680

Supplementary file Size Download File type/resource
GSM8033086_WT_NR4A3_CUTTag_REP2.bw 118.4 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

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