|
| Status |
Public on Aug 07, 2021 |
| Title |
WT_rnc_repeat1 |
| Sample type |
SRA |
| |
|
| Source name |
intrahepatic cholangiocarcinoma cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: wild type
|
| Treatment protocol |
Mettl1 gene knockdown was mediated by short hairpin RNA.
|
| Growth protocol |
ICC cell lines were cultrued in RMPI 1640 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, TruSeq Ribo Profile (Mammalian) Library Prep Kit and the NEBNext® Small RNA Library Prep Set.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MGISEQ-2000RS |
| |
|
| Description |
RNC_mRNA_expression.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 (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 Reads per kilo base per million mapped reads (RPKM) using edegR.
For Ribo-Seq data analysis, Adapter sequences were trimmed and low quality sequences (Q30) were discarded using trim_galore. The sequences with length of at least 25nt were further aligned to human rRNA and tRNA index constructed from Ensembl (Release 91) and GtRNAdb databases , respectively. The remaining reads were aligned to the UCSC canonical known gene transcripts of the human reference genome (hg38) using bowtie with a maximum one mismatch allowed.
|
| |
|
| Submission date |
Jun 15, 2021 |
| Last update date |
Aug 07, 2021 |
| Contact name |
Haining Liu |
| E-mail(s) |
liuhn6@mail2.sysu.edu.cn
|
| Phone |
17820523342
|
| Organization name |
The first affiliated hospital of sun yat-sen university
|
| Street address |
Zhongshan road 2
|
| City |
Guangzhou |
| ZIP/Postal code |
510000 |
| Country |
China |
| |
|
| Platform ID |
GPL30209 |
| Series (1) |
| GSE161319 |
N7-methylguanosine tRNA modification enhances oncogenic mRNA translation and promotes intrahepatic cholangiocarcinoma progression |
|
| Relations |
| BioSample |
SAMN19716269 |
| SRA |
SRX11154147 |
