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| Status |
Public on May 18, 2024 |
| Title |
control1 |
| Sample type |
SRA |
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| Source name |
Epithelial tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Epithelial tissue
cell line: HFF
cell type: Human Fibroblast
genotype: WT
treatment: Control
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| 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.
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Description |
Control, replicate1
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| 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
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| Submission date |
Apr 29, 2024 |
| Last update date |
May 18, 2024 |
| Contact name |
haimei wen |
| E-mail(s) |
hudie.luoluo@gmail.com
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| Organization name |
Fudan university
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| Department |
Collaborative Innovation Center of Genetics and Development,
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| Lab |
Nilab
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| Street address |
SongHu road 2005
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| City |
Shanghai |
| ZIP/Postal code |
200433 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE266081 |
Cellular senescence induced by down-regulation of PTBP1 correlates with exon skipping of mitochondrial related gene NDUFV3 |
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| Relations |
| BioSample |
SAMN41101416 |
| SRA |
SRX24385461 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8240258_plko-1-1_comp.combined.gtf.gz |
6.7 Mb |
(ftp)(http) |
GTF |
| GSM8240258_plko_1_1_hits.bam.bw |
36.5 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
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