|
| Status |
Public on Nov 06, 2024 |
| Title |
LEO1 KO 4sUDRB-seq 10min rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
genotype: LEO1 KO
|
| Treatment protocol |
10 million cells were used for each experiment. After DRB (Sigma, cat. no. D1916) treatment and 4sU (Sigma, cat. no. T4509) incorporation, total RNA was extracted.
|
| Growth protocol |
Human cells K562 were cultured in 90% DMEM + 10% FBS+ 2% Penicillin/Streptomycin + 2 mM L-Glutamine.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After RNA biotinylation and free biotin removal, biotinylated RNA was purified by streptavidin-coupled Dynabeads (Thermo, cat. no. 11205D). rRNA was depleted before library construction. Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
Sequencing libraries were constructed by following the Illumina TruSeq RNA Library preparation protocol.
4sU-DRB-seq
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were trimmed for adaptor sequence and low-complexity or low-quality sequence were filtered using fastp v0.13.1 with default parameters. 4sUDRB-seq reads were aligned using bowtie2 v2.3.4.1.
Normalized aboundency in each 50-bp genomic bin were generated into bigWig file using deepTools bamCoverage command with parameter --normalizeUsing CPM.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files contains normalized read count (CPM, in 50-bp bins).
|
| |
|
| Submission date |
Nov 08, 2021 |
| Last update date |
Nov 06, 2024 |
| Contact name |
Aiwei Wu |
| E-mail(s) |
aiwei.wu@sjtu.edu.cn
|
| Organization name |
Shanghai Jiao Tong University
|
| Department |
School of Life Sciences and Biotechnology
|
| Lab |
Ming Yu
|
| Street address |
800 Dongchuan Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200240 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE188410 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation [4sUDRB-seq] |
| GSE188417 |
The PAF1 Complex Regulates Transcriptional Termination and Reinitiation |
|
| Relations |
| BioSample |
SAMN22984385 |
| SRA |
SRX13056987 |
