|
| Status |
Public on Jan 29, 2024 |
| Title |
HEK293T,RESTART v3-TAG-RNA,rep 2 |
| 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 global RNA expression level in wildtype HEK293T cells with RESTART v3-TAG treatment
|
| Data processing |
Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.7) for quality control and adapter trimming. The key parameters were: -q 20 --phred33 --stringency 3 --length 20. Trimmed reads were down-sampled to 30Mb using seqtk. The key parameters were: seqtk sample -s 100 30000000.
Then the cleaned reads were mapped to the human genome (hg38, NCBI Refseq) using STAR (version 2.7.10b) with default parameters. Mapped reads were filtered by samtools (version 1.14). The key parameters were: samtools view -f 3 -F 256.
The gene counts were quantified by HTSeq (version 1.14), and genes with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The gene expression level was quantified by FPKM.
Assembly: GRCh38
Supplementary files format and content: Raw sequencing reads were subjected to Trim_galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) software (version 0.6.7) for quality control and adapter trimming. The key parameters were: -q 20 --phred33 --stringency 3 --length 20. Trimmed reads were down-sampled to 30Mb using seqtk. The key parameters were: seqtk sample -s 100 30000000. Then the cleaned reads were mapped to the human genome (hg38, NCBI Refseq) using STAR (version 2.7.10b) with default parameters. Mapped reads were filtered by samtools (version 1.14). The key parameters were: samtools view -f 3 -F 256. The gene counts were quantified by HTSeq (version 1.14), and genes with low biological repeatability (log2 fold change(replication 1/replication 2)>1) were discarded. The gene expression level was quantified by FPKM.
|
| |
|
| 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) |
| GSE237631 |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons [RNA-seq] |
| GSE237633 |
Near-cognate tRNAs increase the efficiency and precision of pseudouridine-mediated readthrough of premature termination codons |
|
| Relations |
| BioSample |
SAMN36521040 |
| SRA |
SRX21063998 |
