|
| Status |
Public on May 18, 2024 |
| Title |
PTBP1-sh3-KO2 |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Epithelial tissue
cell line: HFF
cell type: Human Fibroblast
genotype: PTBP1 Knock down
treatment: PTBP1 sh3 Knock down
|
| Growth protocol |
Cells were cultured in DMEM (Gibco) supplemented with 15% (HFF cells) and 10% (HEK293T cells) FBS (Gibco) at 37°C in a humidified, 5% CO2 incubator. When the cell confluence reached about 95%, the cells were sub-cultured at 1:4.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA were isolated with TRIzol reagent according to manufacturer's instructions (Invitrogen, 15596026). Then, RNA was reversely transcribed into cDNA with oligo-(dT)23 VN primer and (or) random hexamers using HiScript II 1st Strand cDNA Synthesis Kit (+gDNA wiper) (Vazyme, R212). Gene expression at the RNA level was quantified by qRT-PCR using 2× SYBR mix (Vazyme, Q711). GAPDH’s RNA expression level served as an internal control.
Total RNA was extracted with TRIzol reagent (Invitrogen, 15596018) according to the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
PTBP1 sh3 knock down, replicate2
|
| Data processing |
reads were mapped to hg38 using STAR
bam file convert to bw file using deeptools
Assembly: hg38
Supplementary files format and content: bw file for reads peak
|
| |
|
| Submission date |
Apr 29, 2024 |
| Last update date |
May 18, 2024 |
| Contact name |
haimei wen |
| E-mail(s) |
hudie.luoluo@gmail.com
|
| Organization name |
Fudan university
|
| Department |
Collaborative Innovation Center of Genetics and Development,
|
| Lab |
Nilab
|
| Street address |
SongHu road 2005
|
| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE266081 |
Cellular senescence induced by down-regulation of PTBP1 correlates with exon skipping of mitochondrial related gene NDUFV3 |
|
| Relations |
| BioSample |
SAMN41101426 |
| SRA |
SRX24385463 |
