|
| Status |
Public on Jan 03, 2022 |
| Title |
VL_SkM_12w_RT_SWOLL41 |
| Sample type |
genomic |
| |
|
| Source name |
baseline_vastus lateralis_12w_RT_Protein Metabolism Research Laboratory; Stuart M. Phillips, PhD; Department of Kinseiology, McMaster University, Hamilton, Ontario, CAN
|
| Organism |
Homo sapiens |
| Characteristics |
age: 21
disease: healthy
Sex: male
tissue: Skeletal Muscle (Vastus Lateralis)
|
| Treatment protocol |
None
|
| Growth protocol |
None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from vastus lateralis skeletal muscle tissue embedded in OCT. Tissue samples were equilibrated to room temperature and removed from OCT and rinsed in 1x phosphate buffered saline. DNA was the extracted using Qiagen DNeasy Blood and Tissue Kits (Qiagen, Venlo, Netherlands; Cat. No: 69506) in accordance with the manufacturers specifications.
|
| Label |
Streptavidin Phycoerythrin (SAPE)
|
| Label protocol |
As per manufacturer's specificatin (Thermo Fisher)
|
| |
|
| Hybridization protocol |
DNA was assayed in accordance with manufacturer's specification (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018119_702989_Axiom2_96F_Man_QR.pdf)
|
| Scan protocol |
DNA was assayed in accordance with manufacturer's specification (https://assets.thermofisher.com/TFS-Assets/LSG/manuals/MAN0018119_702989_Axiom2_96F_Man_QR.pdf)
|
| Description |
healthy college-aged male
|
| Data processing |
Raw data files wire analyzed using Axiom Analysis Suite v4.0.3.3 (Thermo Fisher Scientific). QC of genotype data was completed using Plink (V. 1.9) controlling for high levels of missingness, minor allele frequency, and violations of the Hardy-Weinberg equilibrium rule. Genome-wide p-value distribution was evaluated using Q-Q plots of observed versus expected -log10 p-value.
Genotype Call (SNP call): AA, AB, BB, NC, and NoCall
|
| |
|
| Submission date |
Mar 22, 2021 |
| Last update date |
Jan 03, 2022 |
| Contact name |
Christopher G. Vann |
| E-mail(s) |
christopher.vann@duke.edu
|
| Organization name |
Duke University School of Medicine
|
| Department |
Molecular Physiology Institute
|
| Lab |
Kraus Lab
|
| Street address |
300 N. Duke St
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27701 |
| Country |
USA |
| |
|
| Platform ID |
GPL29894 |
| Series (1) |
| GSE169300 |
Axiom PMDAr.6 SNP array for human skeletal muscle samples |
|
| Relations |
| BioSample |
SAMN17032790 |
