|
| Status |
Public on Mar 17, 2020 |
| Title |
SMMC7721-shYTHDF2 |
| Sample type |
SRA |
| |
|
| Source name |
Liver cancer cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hepatocellular carcinoma
passage: 15-18
genotype: YTHDF2 knockdown
|
| Growth protocol |
SMMC7721-Ctrl and SMMC-shYTHDF2 cells were seeded at 1-5*10^5 in a 10cm dish and cultured in DMEM supplemented with 10% FBS and 1%P/S.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were washed three times with PBS before RNA was harvested using Trizol reagent. ΒioTeke RNA extraction Kit (Cat#RP4002) was used with 1 ug of total RNA for the construction of sequencing libraries.
For RNA-sequencing, ribosomal RNA was removed and strand-specifc sequencing libraries were generated using KAPA Riboerase-RNA Hyper Prep Kit following manufacture’s recommendations. After proper quality control steps, the libraries were sequenced on illumina HiSeq platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Sequence reads were aligned to the human genome GRCh19 with TopHat2
the resulting alignment files were reconstructed with Cufflinks
An adjusted P value< 0.05 and fold change>2 was used as the cut-offfor significantly differentially expressed genes using Cuffdiff
Genome_build: the human genome GRCh19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Sep 29, 2018 |
| Last update date |
Mar 17, 2020 |
| Contact name |
Zhenjun Zhao |
| E-mail(s) |
g-l-o-r-y@sjtu.edu.cn
|
| Organization name |
Renji Hospital, Shanghai Jiao Tong University, School of Medicine
|
| Street address |
1630 Dongfang Road, Puundong New District, Shanghai, China
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE120659 |
Next Generation Sequencing Facilitates Quantitative Analysis of SMMC7721 shYTHDF2 and shCtrl transcriptomes. |
|
| Relations |
| BioSample |
SAMN10145531 |
| SRA |
SRX4778010 |
