|
| Status |
Public on Mar 31, 2023 |
| Title |
Z1_shen |
| Sample type |
SRA |
| |
|
| Source name |
Perillen-treated Hyperuricemia mice group
|
| Organism |
Mus musculus |
| Characteristics |
group: Hyperuricemia mice group
treatment: Perillen
age: 11weeks
breed: KunMing mice
tissue: kidney
|
| Treatment protocol |
Perillen was dissolved in normal saline and administered i.g. once a day for 14 days at doses of 10mg/kg.
|
| Growth protocol |
The animals were housed in a temperature-controlled animal room (24 ± 2 ℃) with a relative humidity of 60-80%.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Kidney were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava software used for basecalling.
Read quality was checked for each sample using fastx_toolkit_0.0.14.
High-quality reads were then imported into HISAT2 to get mapped reads.
Mapped Reads are spliced using StringTie software, based on the selected reference genome sequence.
The functional annotations of gene/transcript in NR, Swiss-PROt, Pfam, EggNOG, GO and KEGG were summarized.
RSEM software conducts quantitative analysis of gene and transcript expression levels respectively. The quantitative index is TPM, which refers to the number of transcripts as the unit of calculation.
After obtaining the Read Counts of genes/transcripts, DESeq2, DEGseq or edgeR can be used to conduct sample or intergroup gene/transcript differential expression analysis for multiple (≥2) items to identify the differentially expressed genes/transcripts.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample ...
Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Jan 20, 2021 |
| Last update date |
Mar 31, 2023 |
| Contact name |
zhu jie |
| E-mail(s) |
1811210064@bjmu.edu.cn
|
| Phone |
18940822582
|
| Organization name |
北京大学医学部
|
| Street address |
北京市海淀区学院路38号
|
| City |
北京 |
| ZIP/Postal code |
100083 |
| Country |
China |
| |
|
| Platform ID |
GPL13112 |
| Series (2) |
| GSE165173 |
A Deep Learning based Efficacy Prediction System for Drug Discovery [Perillen] |
| GSE165175 |
A Deep Learning based Efficacy Prediction System for Drug Discovery |
|
| Relations |
| BioSample |
SAMN17388209 |
| SRA |
SRX9902789 |
