|
| Status |
Public on Feb 06, 2023 |
| Title |
PRAISE-PUS7KO-untreated_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
genotype: PUS7KO
treatment: untreated
|
| Growth protocol |
HEK293T were cultured in DMEM medium (Corning) supplemented with 10% (v/v) FBS (Gibco), 1% GlutaMAX (Gibco) and 0.5% penicillin/streptomycin (Gibco) at 37 °C with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol (Life technologies) followed by isopropanol precipitation, according to the manufacturer’s instructions (Invitrogen).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
Illumina PE150
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
trimiming using cutadapt
mapping using HISAT2 and then tailored alignment
remove multiple mapping
converting bam into bw using bamCoverage
Assembly: hg38
Supplementary files format and content: bw files including mapping result data
|
| |
|
| Submission date |
Sep 29, 2022 |
| Last update date |
Feb 08, 2023 |
| Contact name |
Jiang Zhe |
| E-mail(s) |
[email protected]
|
| Phone |
010-62752895
|
| Organization name |
Peking University
|
| Department |
School of Life Sciences
|
| Lab |
Chengqi Yi lab
|
| Street address |
No. 5 Yiheyuan Road, Haidian District
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE212210 |
Quantitative profiling of pseudouridylation landscape in the human transcriptome |
|
| Relations |
| BioSample |
SAMN31095411 |
| SRA |
SRX17751040 |
