|
| Status |
Public on Oct 04, 2016 |
| Title |
Control shRNA3 |
| Sample type |
SRA |
| |
|
| Source name |
BGC823_Control shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: BGC823
cell type: human gastric cancer cells
passage: 16-19
transfected with: nonspecific shRNA virus
|
| Treatment protocol |
The shRNA adenovirus against human lncRNA GAS1 were introduced into the BGC823 gastric cells, while nonspecific shRNA virus was used as negative controls.
|
| Growth protocol |
The human gastric cancer cells BGC823 were cultured in RPMI-1640 medium (Gibco, USA) supplemented with 10 % fetal bovine serum at 37 °C in an atmosphere of 5 % CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA of BGC23 cells with different treatment was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 3
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced readsmapped to hg19 whole genome using TopHat v2.0.1
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each group (C1=control; C2=GAS1-shRNA)
|
| |
|
| Submission date |
Dec 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Haoyan Chen |
| Organization name |
Renji Hospital
|
| Street address |
145 Shandong Road
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200001 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE63764 |
A novel lncRNA GAS1 promotes gastric carcinogenesis and acts as a modular scaffold of WDR5 and KAT2A complexes to specify the histone modification pattern [RNA-seq] |
| GSE63765 |
ChIP-seq and RNA-seq in BGC823 cells after downregulation of GAS1 expression |
|
| Relations |
| BioSample |
SAMN03247759 |
| SRA |
SRX792207 |
