|
| Status |
Public on Feb 06, 2023 |
| Title |
PRAISE-DKC1KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
genotype: DKC1 stable knockdown
treatment: PRAISE
fraction: mRNA
|
| 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 (Invitrogen) followed by isopropanol precipitation, according to the manufacturer’s instructions. For PolyA+ RNA isolation, size selection was first performed using MEGAclear Transcription Clean-Up Kit (Ambion) to deplete small RNA, and RNA was subsequently purified with two sequential rounds of polyA tail purification using oligo (dT)25 Dynabeads (Invitrogen). Small RNA fractions were collected from the flow-through of MEGAclear Transcription Clean-Up Kit.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols. tRNA libraries for RNA-seq were prepared using eCLIP library construction method.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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 |
Feb 06, 2023 |
| 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 |
SAMN33143030 |
| SRA |
SRX19298161 |
