|
| Status |
Public on Dec 31, 2020 |
| Title |
SNU449 shNC |
| Sample type |
SRA |
| |
|
| Source name |
SNU449 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SNU449
cell type: liver cancer cell
transfection: Perform sequence after transfection with FZD2 shNC for 7 days
gentoype: Negative control
|
| Treatment protocol |
SNU449 cells (3×105/well) were seeded in 6-well plates and transfected with shRNA expressing lentivirus for 1 week
|
| Growth protocol |
Human prostate cancer cells SNU449 were cultured in RPMI1640 medium supplemented with 10% FBS and incubated at 37℃ in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA for RNA sequencing (RNA-seq) was isolated from SNU449 cells transfected with shRNA expressing lentivirus for 1 week. After extracting from cells, total RNA was quantified and integrity measured by BioAnalyzer 2100. Oligo (dT) magnetic beads were used to select mRNA with polyA tail and the target RNA was obtained after purification.
Fragmented the target RNA and reversed transcription to double-strand cDNA (dscDNA) by N6 random primer. Then End repair was performed. The dscDNA was ligated with adaptor and amplified by PCR. Denatured the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Data processing |
Data Filtering: 1) Remove reads with adaptors; 2) Remove reads in which unknown bases are more than 10%; 3) Remove low quality reads
Reads Mapping performed by Bowtie2 to map clean reads to reference gene and use HISAT to reference genome
Gene quantified by FPKM
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 27, 2018 |
| Last update date |
Jan 01, 2021 |
| Contact name |
Dinghua Yang |
| E-mail(s) |
nfyangdh@163.com
|
| Organization name |
Nanfang Hospital
|
| Street address |
1838 North Guangzhou Avenue
|
| City |
Guangzhou |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE112363 |
Next Generation Sequencing Facilitates Quantitative Analysis of FZD2 Knockdown/Control SNU449 Cell Line Transcriptomes |
|
| Relations |
| BioSample |
SAMN08799517 |
| SRA |
SRX3851177 |
