|
| Status |
Public on Jan 15, 2024 |
| Title |
KYSE30 cells, OE_circ-PDE5A 1 |
| Sample type |
SRA |
| |
|
| Source name |
KYSE30 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KYSE30 cells
cell type: Esophageal squamous carcinoma cells
treatment: OE_circ-PDE5A
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from circ-PDE5A overexpressing or control ESCC cells using the TRIzol Total RNA Isolation Kit (Takara, USA), followed by strict quality control of the RNA samples.
Ribosomal RNA was removed from total RNA to enrich for mRNA, and RNA was reverse transcribed to cDNA using random primers. Purified double-stranded cDNA was subjected to end repair, A-tailed, and ligated to sequencing connectors. The cDNAs of around 250-300 bp were sieved on AMPure XP beads and amplified by PCR. The PCR products were purified again using AMPure XP beads to obtain the final library.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
preliminary quantification was performed using a Qubit 2.0 Fluorometer to dilute the library to 1.5 ng/ul. The library insert size was then determined using an Agilent 2100 bioanalyzer, and experimental RT-qPCR was performed to accurately quantify the effective concentration of the library (the effective concentration of the library was above 2nM) to ensure the quality of the library. After the libraries passed the quality control, different libraries were pooled according to the effective concentration and target downstream data volume for Illumina sequencing.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
|
| |
|
| Submission date |
Dec 15, 2023 |
| Last update date |
Jan 15, 2024 |
| Contact name |
kai lei |
| E-mail(s) |
[email protected]
|
| Organization name |
Sun Yat-sen Memorial Hospital, Sun Yat-sen University
|
| Department |
Department of Thoracic Surgery
|
| Street address |
107 Yan Jiang West Road
|
| City |
Guangzhou |
| ZIP/Postal code |
510120 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE250323 |
A novel regulator of the PI3K/AKT pathway encoded by circ-PDE5A inhibits esophageal squamous carcinoma progression by promoting USP14-mediated deubiquitination of PIK3IP1 |
|
| Relations |
| BioSample |
SAMN38859070 |
| SRA |
SRX22906299 |
