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| Status |
Public on Dec 01, 2023 |
| Title |
SC103973 |
| Sample type |
SRA |
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| Source name |
ascending aorta
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| Organism |
Homo sapiens |
| Characteristics |
disease state: normal ascending aorta
age: adult
tissue: ascending aorta
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
For isolation of primary cells from human artery tissues,aorta samples were chopped into small pieces and digested with Aorta Dissociation Enzyme stock solution (125 mg/ml Collagenase type I in high glucose DMEM) for 2 hour at 37°C. After incubation, the digested aorta were rigorously pipetted up and down for several times, and then filtered through a 70-μm cell strainer into 15ml tubes. Then, isolated cells were maintained in 10% FBS/DMEM.
RNA was extracted from cells, and libraries were generated using the using the ICELL8 platform (Takara) according to the manufacturer’s instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
single cells
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| Data processing |
For single cell RNA-Seq analysis,reads were filtered by cutadapt with phred score threshold 20 and trimmed Ns.
Reads were mapped to human genome (hg38, UCSC) via STAR (2.5.2b).
Clean reads with same UMI were combined and then annotated to ensemble genes by featureCounts.
Genome_build: hg38
Supplementary_files_format_and_content: csv,gene expression matrix for single cell RNASeq
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| Submission date |
Jan 19, 2020 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Li Wang |
| Organization name |
NIH
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| Street address |
111 T.W. Alexander Dr
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| City |
Durham |
| ZIP/Postal code |
27709 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE143921 |
Vascular smooth muscle cell senescence instigates thoracic aortic aneurysm |
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| Relations |
| BioSample |
SAMN13884428 |
| SRA |
SRX7582265 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4276645_103973_merged.genematrix.csv.gz |
4.6 Mb |
(ftp)(http) |
CSV |
| GSM4276645_103973_merged.report.csv.gz |
65.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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