|
| Status |
Public on Sep 20, 2020 |
| Title |
MCF7_S_3 |
| Sample type |
RNA |
| |
|
| Source name |
Cultured MCF-7 spheroid cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell source: Estrogen-dependent human breast adenocarcinoma
culture condition: Spheroid
|
| Growth protocol |
The monolayer and spheroid MCF-7 cells were cultured in tissue culture-treated flasks and as suspension spheroid respectively. Both are maintained in 5% CO2 humidified incubator.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA with retention of small RNAs from the cells were extracted using miRNeasy kit according to the manufacturer's instructions
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (FlashTaq Biotin HSR RNA Labeling kit, Affymetrix, 2013).
|
| |
|
| Hybridization protocol |
Following ligation, 21.5ul of biotin-labeled sample were hybridized for 16 hours at 48C on GeneChip miRNA 4.0 arrays.GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the GeneChip Scanner 3000 7G
|
| Description |
Gene expression data of MCF-7 spheroid
|
| Data processing |
The raw CEL files were processed using the Affymetrix Expression Console Software (build 1.3.1) with microRNA arrays-RNA + DABG-Human only normalization to produce CHP files for each of the 6 samples. The six CHP files were then imported into the Affymetrix Transcriptome Analysis Console (TAC) 3.0 (build 3.0.0.466) using the Gene Level Differential Analysis option. Three conditions were created using TAC. One-way between-subject ANOVA (unpaired) were used as the algorithm options, and the default filter criteria was fold change >2 and <-2. The ANOVA p-value was set at <0.05.
|
| |
|
| Submission date |
Apr 20, 2015 |
| Last update date |
Sep 20, 2020 |
| Contact name |
norlaily mohd ali |
| E-mail(s) |
norlailyma@gmail.com
|
| Organization name |
Universiti Tunku Abdul Rahman
|
| Department |
Faculty of Medicine and Health Sciences
|
| Street address |
Universiti Tunku Abdul Rahman, Jln Sg Long
|
| City |
Cheras |
| State/province |
Selangor |
| ZIP/Postal code |
43000 |
| Country |
Malaysia |
| |
|
| Platform ID |
GPL19117 |
| Series (1) |
| GSE68031 |
miRNA transcriptome profiling of spheroid-enriched cells with cancer stem cell properties in human breast MCF-7 cell line. |
|
