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| Status |
Public on Jun 22, 2024 |
| Title |
Control-Aortic-Wall-3 |
| Sample type |
SRA |
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| Source name |
Aortic Wall
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Aortic Wall
treatment: Control
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated from human AAA wall, accompanying thrombi, and control aortic walls tissue with the commercially available NucleoSpin® RNA kit (Macherey-Nagel REF 740955) with several modifications. Tissue was thawed on ice and transferred to BeadBugÔ prefilled tubes (Benchmark Scientific Triple-Pure High Impact Zirco nium Beads Item D1032-15). Tubes were filled with 1 mL QIAzol Lysis Reagent (QIAGEN Cat No. 79306) and homogenized with a BeadBugÔ Microtube Homogenizer (Benchmark Scientific) after which 200 μL of chloroform were added. Samples were vortexed and left to sit at room temperature for 2 – 3 minutes. Samples were then centrifuged at 12,000 X g for 15 minutes at 4°C. The aqueous phase was removed to new tubes and 150 μL isopropyl alcohol was added to each. Following a 10-minute incubation at room temperature, each lysate was loaded onto a NucleoSpin® RNA Column and eluted to RNA. RNA was quantified with a NanoDrop™ 2000 Spectrophotometer (Thermo Scientific) and samples were stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols
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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 |
Data was analyzed using the bioinformatics software CLC Genomics Workbench version 20.0.3 (Qiagen, Hilden, Germany).
Reads were mapped using the following parameters: min. read length fraction = 0.8, min. read similarity fraction = 0.8. mismatch cost = 2, insertion cost = 3, deletion cost = 3, Strand specific = both, Maximum number of hits for a read=10, Expression value= Total counts.
Assembly: hg38
Supplementary files format and content: All processed data files are in an xlsx format containing FPKm values for each sample.
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| Submission date |
Jun 14, 2024 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Tyler Benson |
| E-mail(s) |
bensonte@ucmail.uc.edu
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| Phone |
24488946641
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| Organization name |
University of Cincinnati
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| Lab |
Owens
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| Street address |
CVC 3976 231 Albert Sabin Way
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45267 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE269845 |
Soluble Glycoprotein VI Predicts Abdominal Aortic Aneurysm Growth Rate and is a Novel Therapeutic Target |
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| Relations |
| BioSample |
SAMN41833123 |
| SRA |
SRX25055236 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8328836_Control-Aortic-Wall-3_genes.xlsx |
1.3 Mb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
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