|
| Status |
Public on Jun 26, 2021 |
| Title |
polyribosome associated mRNA-seq-MHCC97H_shMETTL1-2_Input_repeat 3 |
| Sample type |
SRA |
| |
|
| Source name |
hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Mettl1 knockdown
sample type: RNA-Seq
|
| Treatment protocol |
Mettl1 gene knockdown was mediated by short hairpin RNA.
|
| Growth protocol |
HCC cell lines were cultrued in DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃. C57 mice were taken care in SPF-class laboratory animal housing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA samples were isolated with Trizol following the manufacturer’s instructions. small RNAs (<200nt) were first purified using the mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
Libraries were prepared according to Illumina's instructions accompanying the TrueSeq Stranded mRNA library preparation kit and the NEBNext Small RNA Library Prep Set.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
DNBSEQ-G400 |
| |
|
| Description |
FPKM_polyribosome associated mRNA-seq.txt
|
| 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 (GRCh38) using Bowtie2. 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 fractions per kilo base per million mapped reads (FPKM) using edegR.
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). The read counts of tRNA are normalized as reads per million (RPM) by the total number of small RNA reads that are matched to tRNAs in each sample.
|
| |
|
| Submission date |
May 14, 2021 |
| Last update date |
Jun 26, 2021 |
| Contact name |
Wanjie Zhu |
| E-mail(s) |
zhuwanj@mail2.sysu.edu.cn
|
| Phone |
15889961606
|
| Organization name |
Sun Yat-sen University
|
| Street address |
Zhongshan er road
|
| City |
Guangzhou |
| State/province |
Guangdong |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL28038 |
| Series (1) |
| GSE174492 |
METTL1 promotes hepatocarcinogenesis via m7G tRNA modification dependent translation control |
|
| Relations |
| BioSample |
SAMN19195328 |
| SRA |
SRX10895533 |
