|
| Status |
Public on Apr 17, 2019 |
| Title |
SGC_7901_DDP |
| Sample type |
SRA |
| |
|
| Source name |
SGC7901 cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: gastric cancer cell
transfection: Perform sequence after SGC7901/DDP cells were continuously exposed to increasing concentration of cisplatin
cell line: SGC7901
gentoype: DDP resistant
|
| Treatment protocol |
SGC7901/DDP cells were continuously exposed to increasing concentrations of cisplatin
|
| Growth protocol |
Human gastric cancer cells SGC7901 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 SGC7901 cells with different treatment. 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 |
Nov 05, 2018 |
| Last update date |
Apr 17, 2019 |
| Contact name |
Libo Li |
| Organization name |
Dongguan People's Hospital
|
| Department |
Department of General Surgery
|
| Street address |
No.3 Wan Road, Dongguan, Guangdong
|
| City |
Dongguan |
| ZIP/Postal code |
523000 |
| Country |
China |
| |
|
| Platform ID |
GPL23227 |
| Series (1) |
| GSE122130 |
Next generation sequencing analysis of mRNA profile in cisplatin-resistant gastric cancer cell line SGC7901 |
|
| Relations |
| BioSample |
SAMN10374630 |
| SRA |
SRX4977333 |
