|
| Status |
Public on Feb 01, 2023 |
| Title |
DIAC007 |
| Sample type |
SRA |
| |
|
| Source name |
Chronic foot ulcer
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: skin
tissue: Chronic foot ulcer
disease: Diabetic
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Skin wounds specimens were collected in PBS with 1% Pen/Strep. Tissues were cleaned with 10% betadine, twice in 70% ethanol, and twice in PBS. Tissues digestion followed protocol in Sandoval-Schaefer & Phan et al. to achieve single cell suspensions in DMEM with 700-1200 cells per uL.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: H5 matrix, seurat object and h5ad of combined processed files.
|
| |
|
| Submission date |
Jan 29, 2023 |
| Last update date |
Feb 01, 2023 |
| Contact name |
Ryan Roy Driskell |
| E-mail(s) |
ryan.driskell@wsu.edu
|
| Phone |
5093353807
|
| Organization name |
Washington State University
|
| Department |
Molecular Biosciences
|
| Lab |
Driskell
|
| Street address |
100 Dairy Rd. BLS 202A
|
| City |
Pullman |
| State/province |
Washington |
| ZIP/Postal code |
99164 |
| Country |
USA |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE223964 |
Gene expression profile as single cell level of chronic diabetic foot ulcers and chronic non-diabetic foot ulcer |
|
| Relations |
| BioSample |
SAMN32954015 |
| SRA |
SRX19210660 |
