|
| Status |
Public on Sep 14, 2023 |
| Title |
kidney cancer tissue rep1 |
| Sample type |
SRA |
| |
|
| Source name |
kidney cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: kidney cancer tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNAiso Plus (Takara, 9109) according to manufacturer’s protocol.
Sequencing libraries were prepared using the VAHTS Stranded mRNA-Seq Library Prep Kit (Vazyme, NR602-02) according to manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-T7 |
| |
|
| Data processing |
FastQC (version: 0.11.5) was used to assess the quality of raw reads, and FASTP (version: 0.23.2) was used to filter out the low-quality bases and adapter sequences.
The clean reads were aligned to the hg19 using BWA-MEM (version: 0.7.17) with default parameters and sorted by Samtools (version: 1.15.1).
Gene expression levels were assessed using featureCounts51 (version: 2.0.0). Differential gene expression analysis was performed using the DEseq252 (version: 1.20.0) package.
The analysis outlined above was conducted with a complete pepline in https://github.com/GangCaoLab/NGS-pipelines/tree/master/RNA-Seq.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include differential gene expression analysis result
|
| |
|
| Submission date |
Jun 01, 2022 |
| Last update date |
Sep 14, 2023 |
| Contact name |
zou yanyan |
| E-mail(s) |
yyzou0721@outlook.com
|
| Organization name |
HZAU
|
| Street address |
SHIZISHAN
|
| City |
WuHan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL29480 |
| Series (2) |
| GSE205281 |
MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell [RNA-Seq] |
| GSE205293 |
MGA-seq is an efficient tool for genetic variants and extrachromosomal DNA detection in cancer cell |
|
| Relations |
| BioSample |
SAMN28813345 |
| SRA |
SRX15557397 |
