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| Status |
Public on May 10, 2024 |
| Title |
VSMC, WT, Day1,rep2 |
| Sample type |
SRA |
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| Source name |
Aorta
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| Organism |
Mus musculus |
| Characteristics |
tissue: Aorta
cell line: VSMC
cell type: Primary
genotype: WT
treatment: none
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| 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.
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| Growth protocol |
Cells were cultured in DMEM/F12 medium containing 10 % fetal bovine serum (FBS) and 1 % penicillin-streptomycin, and 10 mM β-GP.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Jan 24, 2024 |
| Last update date |
May 10, 2024 |
| Contact name |
Wenqi Ma |
| E-mail(s) |
wenqiM@hotmail.com
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| Phone |
+8615905172287
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| Organization name |
Shanghai Jiaotong University
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| Street address |
227 Chongqing South Road, Huangpu District, Shanghai, China
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| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
20025 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN39595388 |
| SRA |
SRX23376944 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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