|
| Status |
Public on Jan 29, 2024 |
| Title |
HEK293T,RESTART v3-target TAA,rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
Epithelial
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Epithelial
cell line: HEK293T
cell type: human embryonic kidney 293 cells
genotype: WT
|
| Treatment protocol |
For transfection, 2.5 x 105 of HEK293T cells were seeded on 24-well plates (Corning), and all transfections were conducted when cells reached approximately 80% confluency after 20-24h. The plasmids were extracted using EndoFree Mini Plasmid Kit II (TIANGEN BIOTECH, DP118), and were transfected into cells by Lipofectamine LTX reagent (Invitrogen) supplemented with PLUS reagent (Invitrogen) according to the manufacturer’s instructions.
|
| Growth protocol |
HEK293T cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted from cells using TRIzol reagent (Life Technologies)
RNA libraries were prepared using modified eCLIP library construction, NEBNext Small RNA library kits (NEB) and SMARTer Stranded Total RNA-Seq kits (v3) - Pico Input mammalian (Takara) Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
detect modification level of specific TAA sites in wildtype HEK293T cells with RESTART v3 treatment
|
| Data processing |
First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded.
Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group.
Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters.
The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0).
The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.
Assembly: GRCh38
Supplementary files format and content: First, sequencing reads with the same unique molecular identifier (UMI) were grouped and UMI groups with less than 3 reads were discarded. Then, PCR duplicates were removed by retaining the most consensus sequence in each UMI group. Adapter sequences were further trimmed from deduplicated reads with Trim_galore software (version0.6.7) with default parameters. The 10-nucleotide UMIs were removed by umi_tools (version 1.0.0). The cleaned reads were mapped to the targeted sequences using PRAISE-tool and the deletion rate of target sites was calculated.
|
| |
|
| Submission date |
Jul 18, 2023 |
| Last update date |
Jan 29, 2024 |
| Contact name |
Wenqing Liu |
| E-mail(s) |
puyulwq@163.com, liuwq21@gamils.com
|
| Organization name |
Peking University
|
| Street address |
No. 5 Summer Palace Road, Haidian District, Beijing
|
| City |
Beijing |
| ZIP/Postal code |
010-100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE237629 |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons [Target-seq] |
| GSE237633 |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons |
|
| Relations |
| BioSample |
SAMN36534296 |
| SRA |
SRX21075546 |
