|
| Status |
Public on Dec 31, 2022 |
| Title |
NC_ReD |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung epithelial
treatment: demethylated by ALKB; NaBH4/Aniline induced reduction and cleavage
genotype: negative control
|
| Treatment protocol |
A549 cells were transfected with shRNA for stable knockdown of METTL1. A549 cells transfected with shGFP were used as negative control.
|
| Growth protocol |
A549 cells were cultured in DMEM (Gibco, USA) with 10% fetal bovine serum (FBS, Gibco, USA), 1% streptomycin (Gibco, USA) and 1% Penicillin (Gibco, USA). Cells were cultured in a water-saturated atmosphere under 5% CO2 at 37 °C in an incubator (Thermo Scientific, USA).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted according to TRIzol protocol. Small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to the NEBNext® Small RNA Library Prep Set.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
TRAC-seq
|
| Data processing |
For TRAC-Seq, after adaptor trimming and quality filtering, the clean sequencing data were first mapped to the tRNA sequences using Bowtie2. Then read count for each tRNA was calculated using the method in (Cozen et al., 2015).
Genome_build: hg38
Supplementary_files_format_and_content: txt
|
| |
|
| Submission date |
May 03, 2021 |
| Last update date |
Dec 31, 2022 |
| Contact name |
Ma Jieyi |
| E-mail(s) |
nurch@126.com
|
| Organization name |
SYSU
|
| Street address |
Zhongshan II road
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL28038 |
| Series (2) |
| GSE173760 |
METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression [TRAC-seq] |
| GSE173761 |
METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression |
|
| Relations |
| BioSample |
SAMN18985926 |
| SRA |
SRX10759860 |
