|
| Status |
Public on Aug 11, 2021 |
| Title |
11-2253 Macula Retina |
| Sample type |
SRA |
| |
|
| Source name |
Macula Retina
|
| Organism |
Homo sapiens |
| Characteristics |
age: 83
Sex: F
disease state: early
|
| 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).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RNA-seq data was aligned to the hg38 reference genome using GSNAP (v. ) with default options. Required a mapping quality scofe of ≥30 for each read. Quality control analysis of the aligned data was performed using program RNA-SeQC.
Transcripts were assembled using Cufflinks (v. ). A gene was considered differentially expressed if the false discovery rate (FDR) -adjusted p-value is <0.05.
Genome_build: hg38
Supplementary_files_format_and_content: cxb
|
| |
|
| Submission date |
Jul 27, 2020 |
| Last update date |
Aug 11, 2021 |
| 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) |
|
| Relations |
| BioSample |
SAMN15650254 |
| SRA |
SRX8829885 |
