|
| Status |
Public on May 23, 2021 |
| Title |
RNA-seq-DEX2 |
| Sample type |
SRA |
| |
|
| Source name |
human podocyte
|
| Organism |
Homo sapiens |
| Characteristics |
chip antibody: n/a
tissue: podocyte
|
| Treatment protocol |
Differentiated human podocyte were treated with 1uM DEX for 5 days
|
| Growth protocol |
human podocyte were grown in RPMI-1640 medium with 10% FBS, 1% insulin-transferrin-selenium (ITS) and 1% penicillin-streptomycin at 33. Podocyte began to differentiate at 37.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were treated with 1uM DEX for 5 days.
libraries were constructed according to the Illumina instruction
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
rRNAs depleted RNA
|
| Data processing |
ChIP-seq reads were aligned using Bowtie2 on hg19. Peaks are called using MACS2
RNA-seq reads were aligned using HISAT2 on hg38. Aligned reads were assembled using StringTie and StringTie's output was processed by DESeq2.
HiChIP-seq was processed using HiC-Pro on hg19.
Genome_build: hg19, hg38
|
| |
|
| Submission date |
Jul 30, 2018 |
| Last update date |
May 23, 2021 |
| Contact name |
Jingping Yang |
| E-mail(s) |
[email protected]
|
| Organization name |
Nanjing University
|
| Department |
Medical School
|
| Street address |
22 Hankou Road
|
| City |
Nanjing |
| State/province |
Jiangsu |
| ZIP/Postal code |
210000 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE117888 |
Role of GR in protection of podocyte |
|
| Relations |
| BioSample |
SAMN09742273 |
| SRA |
SRX4488121 |
