|
| Status |
Public on Jul 01, 2024 |
| Title |
116_siSP1 |
| Sample type |
SRA |
| |
|
| Source name |
H116_siSP1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HCT116
genotype/variation: SP1 knockdown
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence with Trimmomatic ( 0.36 ), then mapped to GR38p7 whole genome using Hisat2 ( 2.0.5 ) with parameters ( --rna-strandness RF --fr )
FPKM value of each gene was calculated using cufflinks ( 2.2.1 ),and the read counts of each gene were obtained by htseq-count ( 0.9.1 )
Genome_build: GR38p7
|
| |
|
| Submission date |
Jul 02, 2021 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Zhehui Zhu |
| E-mail(s) |
zhehuizhu0307@126.com
|
| Phone |
18217789586
|
| Organization name |
Shanghai Jiao Tong University School of Medicine
|
| Street address |
Kongjiang Road 1665, Shanghai
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200092 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE179314 |
Identification of differential expressed genes after SP1 or SP3 knockdown in colorectal cancer cells |
|
| Relations |
| BioSample |
SAMN20003686 |
| SRA |
SRX11333336 |
