|
| Status |
Public on Jan 07, 2022 |
| Title |
K562-biological, rep2 |
| Sample type |
RNA |
| |
|
| Source name |
HUVEC cell line & K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUVEC and K562
genotype/variation: K562-HUVEC
|
| Treatment protocol |
The cell lines were infected by RNAi lentiviral vectors of shDIDO1 and shCtrl; K562 and HUVEC cultivated cells
|
| Growth protocol |
The cell lines were maintained using Roswell Park Memorial Institute (RPMI) 1640 medium supplemented with 10% FBS and 1% penicillin/streptomycin at 37°C in a humidified atmosphere containing 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 50-500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16-18 hr at 45 ℃ on GeneChip PrimeView Human Gene Expression Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000.
|
| Description |
Gene expression data from control cell lines
|
| Data processing |
The gene expression profile was preprocessed using Limma package in Bioconductor and Affymetrix annotation files. The background correction, quantile normalization and probe summarization of the microarray data were performed using the Robust Multiarray average algorithm to obtain the gene expression matrix. The cut-off for the background correction was 20%, and the coefficient of variation was 25%. The Benjamini-Hochberg method was used to correct the significant difference level (FDR). The screening criteria for significantly different genes were: |Fold Change|>1.5 and FDR<0.05.
|
| |
|
| Submission date |
Aug 23, 2020 |
| Last update date |
Jan 07, 2022 |
| Contact name |
Shen Zhenglei |
| E-mail(s) |
szl1020@163.com
|
| Organization name |
The third Affiliated Hospital of Kunming Medical University
|
| Street address |
No.519, Kunzhou Road, Xishan District
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650118 |
| Country |
China |
| |
|
| Platform ID |
GPL15207 |
| Series (1) |
| GSE156713 |
Expression data of shDIDO1 and shCtrl HUVEC cell lines |
|
