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| Status |
Public on Aug 13, 2021 |
| Title |
12-0732-PRCS |
| Sample type |
SRA |
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| Source name |
Peripheral Choroid
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| Organism |
Homo sapiens |
| Characteristics |
disease state: Normal
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Aug 12, 2021 |
| Last update date |
Aug 14, 2021 |
| Contact name |
Dwight Edward Stambolian |
| E-mail(s) |
stamboli@pennmedicine.upenn.edu
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| Phone |
2158980305
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| Organization name |
University of Pennsylvania
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| Department |
Opthalmalogy
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| Lab |
Stellar-Chance 313
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| Street address |
422 Curie Blvd.
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| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
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| Relations |
| BioSample |
SAMN20749906 |
| SRA |
SRX11733100 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5516330_12-0732-PRCS_abundances.cxb.gz |
17.5 Mb |
(ftp)(http) |
CXB |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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