|
| Status |
Public on Dec 04, 2019 |
| Title |
Genotype 2 (Tg2) replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Cell line
|
| Organism |
Sus scrofa |
| Characteristics |
cell line: LLC-PK1 cells
overexpression: FLAG-floxP-neo-pH11 with mutant PKD2 (c.T1967G/p.L656W-3)
|
| Treatment protocol |
The different treatments of samples were undertaken by overexpression of different mutants of PKD2 (genotypes) via transfection of different plasmids. FLAG-floxP-neo-pH11 is the plasmid used.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using MiniBEST Universal RNA extraction kit (Takara)
mRNAs were separated with oligo(dT)25 beads from total RNA. mRNA was fragmented and reverse transcribed. The cDNA library was subjected to end repair, poly(A)-tailing, adaptor ligation, and PCR amplification of 12–15 cycles for sequencing library construction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Tg22
|
| Data processing |
Reads were trimmed to remove the bases with low quality and adapter sequences
The trimmed reads were assigned directly to transcripts and counted with Salmon software
Gene expression level was quantified and normalized by Salmon
Differentially expressed genes between 4 genotypes and NC overexpression groups were selected by DESeq2 with Padj. <0.05 and fold change (FC) of >1.2 or <-1.2
Genome_build: 11.1
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
Dec 03, 2019 |
| Last update date |
Dec 05, 2019 |
| Contact name |
Zhe Zhang |
| E-mail(s) |
zhe_zhang@zju.edu.cn
|
| Organization name |
Zhe Jiang University
|
| Street address |
Yuhangtang Road 866
|
| City |
杭州 |
| State/province |
浙江 |
| ZIP/Postal code |
310058 |
| Country |
China |
| |
|
| Platform ID |
GPL26351 |
| Series (1) |
| GSE141355 |
Identification of ADPKD-related Genes and Pathways in the Cells Overexpressing PKD2 |
|
| Relations |
| BioSample |
SAMN13471422 |
| SRA |
SRX7262392 |
