|
| Status |
Public on Nov 20, 2022 |
| Title |
TRAC-Seq_MHCC97H_NC_Alkb_and_NaBH4_Treated |
| Sample type |
SRA |
| |
|
| Source name |
hepatocellular carcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: wild type
sample type: small RNA-TRAC-Seq
|
| Treatment protocol |
Mettl1 gene knockdown was mediated by short hairpin RNA.HCC cells was treated onto 46℃ constant temperature bathwater for 15 minutes.
|
| Growth protocol |
HCC cell lines were cultrued in RMPI 1640 medium or DMEM medium. Cells were grown in a 5% CO2 cell culture incubator at 37℃.
|
| 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 |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
RPKM-TRAC-Seq-MHCC97H.txt
|
| Data processing |
Library strategy: TRAC-Seq
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 |
Apr 01, 2022 |
| Last update date |
Nov 20, 2022 |
| Contact name |
Shenghua Zhu |
| Organization name |
The First Affiliated Hospital, Sun Yat-sen University
|
| Street address |
58 Zhong Shan Road 2
|
| City |
Guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE199966 |
N7-Methylguanosine tRNA modification promotes hepatocellular carcinoma metastasis after insufficient radiofrequency ablation |
|
| Relations |
| BioSample |
SAMN26902628 |
| SRA |
SRX14676318 |
