|
| Status |
Public on Aug 07, 2023 |
| Title |
NC-5 |
| Sample type |
SRA |
| |
|
| Source name |
kidney
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: kidney
strain: Wistar
treatment: administered 0.9percent NaCl
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using TRIzol, 0.2ug of total RNA was used for constuction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNextUltraRNALibraryPrepKitforIllumina(NEB,USA,Catalog#:E7530L)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Index of the reference genome was built using Hisat2 v2.0.5
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: rn6
Supplementary files format and content: excel file includes raw counts for each sample
Supplementary files format and content: excel file includes FPKM values for each sample
|
| |
|
| Submission date |
Aug 07, 2023 |
| Last update date |
Aug 07, 2023 |
| Contact name |
Mindan Sun |
| E-mail(s) |
sunmd@jlu.edu.cn
|
| Organization name |
the First Hospital of Jilin University
|
| Street address |
Street Xinmin 1
|
| City |
Changchun |
| ZIP/Postal code |
130000 |
| Country |
China |
| |
|
| Platform ID |
GPL25947 |
| Series (1) |
| GSE240227 |
Bioinformatics-driven discovery of silica nanoparticles induces apoptosis and renal damage via the unfolded protein response in NRK-52E cells and rat kidney |
|
| Relations |
| BioSample |
SAMN36877634 |
| SRA |
SRX21286394 |
