|
| Status |
Public on Aug 10, 2023 |
| Title |
Retina.Vascular_T407M |
| Sample type |
SRA |
| |
|
| Source name |
Whole Retinal Vasculature
|
| Organism |
Arvicanthis niloticus |
| Characteristics |
tissue: Whole Retinal Vasculature
Sex: Male
acellular capillary density (counts per mm2): 17.84
random blood glucose: 117.2857143
genotype: WT
treatment: No treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs from 28 Nile grass rat vascular samples were isolated using trizol (ThermoFisher #15596018) and chloroform phase separations followed by the RNeasy mini protocol (Qiagen #74106) with optional on-column DNase digestion (Qiagen #79254). One hundred nanograms of total RNA was used to prepare sequencing libraries.
RNA libraries for RNA-seq were prepared using our lab developed LM-seq protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
CRSP tool (https://github.com/pjiang1105/CRSP)
Using CRSP tool to estimate gene expression values
Using mouse protein database as a reference via applying CRSP tool
Assembly: Mapping and gene expression estimation were not based on a particular genome. It was estimated by CRSP tool via mouse protein database
Supplementary files format and content: tab-delimited text files include TPM and Expected Count values for each Sample
|
| |
|
| Submission date |
Dec 11, 2022 |
| Last update date |
Aug 10, 2023 |
| Contact name |
Peng Jiang |
| E-mail(s) |
p.jiang@csuohio.edu
|
| Organization name |
Cleveland State University
|
| Street address |
2121 Euclid Ave
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44115 |
| Country |
USA |
| |
|
| Platform ID |
GPL32935 |
| Series (1) |
| GSE220672 |
Transcriptomic clock predicts vascular changes of prodromal diabetic retinopathy |
|
| Relations |
| BioSample |
SAMN32154206 |
| SRA |
SRX18639755 |
