|
| Status |
Public on Mar 08, 2023 |
| Title |
WT-rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Kidney foot process cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Kidney
|
| Treatment protocol |
Cells were infected with lentivirus vectors that encoded either dlx6-os1 or an empty vector (control) according to the manufacturers’ instruction
|
| Growth protocol |
Cells are cultured using 1640 medium
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA quality and quantity was measured by using nanodrop spectrophotometer (ND-1000, Nanodrop Technologies) and RNA Integrity was determined by gel electrophoresis
Total RNA of each sample was used to prepare the RNA sequencing library 1)RNA fragment；2)Random primed first strand cDNA synthesis；3)dUTP based second strand cDNA synthesis;4)Adaptor ligation and PCR amplification.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
NG-3
|
| Data processing |
Solexa pipeline version 1.8 software used for basecalling.
The sequencing quality of the removed reads was evaluated by FASTQC software.The reference genome was compared by Hisat2 software
The Stringtie software was used to estimate the transcriptional abundance with reference to the annotation information of the official database
Using R software Ballgown, FPKM calculations at the gene level and transcription level were performed, and differences in gene level and transcriptional level expression were calculated, respectively, and differences between samples or groups were screened to express genes
PCA analysis, correlation analysis based on gene expression level, clustering of differential expression genes, GO functional significantity richness analysis, Pathway significant richness analysis
Genome_build: mm10
Supplementary_files_format_and_content: files include FPKM values for each Sample
|
| |
|
| Submission date |
Jan 21, 2021 |
| Last update date |
Mar 08, 2023 |
| Contact name |
Guo Jia |
| Organization name |
The First Affiliated Hospital of Zhengzhou University
|
| Street address |
1 Jianshe Dong Lu, Erqi District,
|
| City |
zhengzhou |
| ZIP/Postal code |
450052 |
| Country |
China |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE165241 |
RNA-seq results of podocytes overexpressed lncRNA Dlx6-os1 |
|
| Relations |
| BioSample |
SAMN17461839 |
| SRA |
SRX9908748 |
