|
| Status |
Public on Jan 18, 2024 |
| Title |
22-3910-tRPE |
| Sample type |
SRA |
| |
|
| Source name |
Periphery Choroid
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Periphery Choroid
disease state: Normal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Donor eyes were obtained from non-diabetic Caucasians at a death-to-preservation interval of <6h. Eyes were stored in RNA later before extraction of RNA. For each eye we dissected macula and periphery from retina and RPE/choroid/sclera resulting in 4 samples per eye. RNA was extracted using the ALLPrep DNA/RNA Mini Kit (Qiagen). All RNA had an RNA integrity number of ≥8.
Strand specific RNA library was prepared from 100 ng total RNA using the Encore Complete RNA-Seq library kit (Nugen Technologies, San Carlos, CA).
RNA-Seq on the Illumina HiSeq 2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
|
| |
|
| Submission date |
Apr 22, 2023 |
| Last update date |
Jan 18, 2024 |
| Contact name |
Dwight Edward Stambolian |
| E-mail(s) |
stamboli@pennmedicine.upenn.edu
|
| Phone |
2158980305
|
| Organization name |
University of Pennsylvania
|
| Department |
Opthalmalogy
|
| Lab |
Stellar-Chance 313
|
| Street address |
422 Curie Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE230348 |
Single cell transcriptomic analysis of human tissue (Retina and RPE/Choroid) |
|
| Relations |
| BioSample |
SAMN34313577 |
| SRA |
SRX20062691 |
