|
| Status |
Public on Dec 20, 2022 |
| Title |
HEK293T,DNMT1_KO,rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293T
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293T
cell type: Human embryonic kidney
genotype: DNMT1_KO
|
| Growth protocol |
DMEM, 15% fetal bovine serum, 2mM glutamine, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
RNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using TrimGalore-0.6.7, discarding reads left with < 20 bp.
Trimmed sequence reads were mapped to hg38 using hisat2 with default setting.
The BAM files were normalized to the total aligned reads (Counts Per Million mapped reads, CPM) with the bamCoverage command from deepTools 3.3.0
Assembly: hg38
Supplementary files format and content: bigwig
|
| |
|
| Submission date |
Dec 20, 2022 |
| Last update date |
Dec 20, 2022 |
| Contact name |
Lijun Xiang |
| E-mail(s) |
xiang-lijun@m.scnu.edu.cn
|
| Phone |
+86-15626099434
|
| Organization name |
South China Normal University
|
| Department |
Guangzhou Key Laboratory of Insect Development Regulation and Application Research
|
| Lab |
Qili Feng lab
|
| Street address |
No.55, West of Zhongshan Avenue
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510631 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE221435 |
DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures [RNA-seq] |
| GSE221437 |
DNA 5-methylcytosine regulates genome-wide formation of G-quadruplex structures |
|
| Relations |
| BioSample |
SAMN32331849 |
| SRA |
SRX18788698 |
