|
| Status |
Public on Mar 31, 2021 |
| Title |
DM_1 |
| Sample type |
SRA |
| |
|
| Source name |
Retinal pigment epithelium
|
| Organism |
Macaca fascicularis |
| Characteristics |
group: Diabetes
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RPE cells were collected from 3 diabetic and 3 control subjects using an ophthalmic 6 spatula. Total RNA was purified using a TRIzol (Thermo Fisher Scientific) in accordance with the manufacturer’s protocol. The RNA sample quality was confirmed by the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were constructed using the TruSeq RNA-Seq kit (Illumina) following the manufacturer’s instructions. After evaluating the quality by Agilent 2100 Bioanalyzer, libraries were pooled and sequenced on Illumina Hiseq X10.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
RNA-seq for diabetic Macaca fascicularis RPE
|
| Data processing |
Illumina Casava(v 1.7) software was used for basecalling.
FastQC (v 0.11.8) were used to removed low-quality reads
Retained reads were then aligned to Macaca 16 fascicularis genome (Macaca_fascicularis_5.0) using STAR (v 2.7.3a) in the pair-end mode with default parameters.
Reads number mapped to each gene was counted using HTSeq (v 0.11.2).
The output matrix from HTSeq was input into the DESeq2 (v 1.26.0) for identification of differentially expressed genes between diabetes group and control group.
Genome_build: Macaca_fascicularis_5.0
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.
|
| |
|
| Submission date |
Nov 02, 2020 |
| Last update date |
Mar 31, 2021 |
| Contact name |
Jiawei Zhong |
| Organization name |
Karolinska Institutet
|
| Department |
Department of Medicine, Huddinge
|
| Lab |
Mikael Rydén & Niklas Mejhert lab
|
| Street address |
Blickagången 16, Flemingsberg
|
| City |
Stockholm |
| ZIP/Postal code |
14182 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL23096 |
| Series (1) |
| GSE160617 |
Extensive Sub-RPE Complement Deposition in a Nonhuman Primate Model of Early Stage Diabetic Retinopathy |
|
| Relations |
| BioSample |
SAMN16623492 |
| SRA |
SRX9417037 |
