|
| Status |
Public on Dec 31, 2022 |
| Title |
A549_RNC_shM1_1 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: lung epithelial
treatment: Ribosome nascent-chain complex-bound mRNAs
genotype: METTL1-knockdown
|
| 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 |
polyA RNA |
| Extraction protocol |
RNA was extracted according to TRIzol protocol.
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
Ribosome nascent-chain complex-bound mRNAs seq
|
| Data processing |
For RNA-Seq data analysis, after adapter trimming and low quality sequence filtering (Q30), the clean reads were mapped to human reference genome (hg38) using Tophat2. The raw counts of reads mapping to the gencode genes (v19) were computed by HTSeq with ‘union’ overlap mode. The raw counts were then normalized as TPM (Transcripts Per Kilobase of exon model per Million mapped reads) using edegR.
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) |
| GSE173750 |
METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression [RNA-seq] |
| GSE173761 |
METTL1/WDR4 mediated tRNA N7-methylguanosine (m7G) modifications promote mRNA translation and lung cancer progression |
|
| Relations |
| BioSample |
SAMN18984149 |
| SRA |
SRX10759792 |
