|
| Status |
Public on Sep 11, 2024 |
| Title |
HCT116 cells, siJOSD1_1 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
cell line: HCT116
cell type: Colorectal cancer
treatment: siJOSD1
|
| Treatment protocol |
HCT116 cells were transfected with Control or siJOSD1.
|
| Growth protocol |
HCT116 cells were plated in 12-well plates at 30% fusion per well
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Lysis of cells with Trizol reagent and harvesting of RNA
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
4
|
| Data processing |
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using ClC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to reference genome using CLc genomc benchwok (parameters-mismath cost: 2 insenion cost: 3 deletion cost. 3 lendh fracion: 0.8 similanity fraction: 0.8
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg19
Supplementary files format and content: Excel files include RPKM values for each Sample
|
| |
|
| Submission date |
Feb 21, 2024 |
| Last update date |
Sep 11, 2024 |
| Contact name |
Zhongbo li |
| E-mail(s) |
a735396587@gmail.com
|
| Phone |
17796793215
|
| Organization name |
Xinxiang medical university
|
| Street address |
jinsuidadao601
|
| City |
Xinxiang |
| State/province |
Henan |
| ZIP/Postal code |
473003 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE256276 |
JOSD1 facilitates colorectal cancer progression via stabilizing YAP |
|
| Relations |
| BioSample |
SAMN40022783 |
| SRA |
SRX23687240 |
