|
| Status |
Public on May 10, 2024 |
| Title |
VSMC, NR4A3KO, H3K18LA Input |
| Sample type |
SRA |
| |
|
| Source name |
Aorta
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Aorta
cell line: VCMC
cell type: Primary
genotype: NR4A3KO
treatment: β-GP
|
| 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) |
| GSE254075 |
Effect of depletion of NR4A3 on vascular calcification [CUTtag_H3K18LA] |
| GSE254078 |
NR4A3耗尽对血管钙化的影响 |
|
| Relations |
| BioSample |
SAMN39594726 |
| SRA |
SRX23376583 |
