|
| Status |
Public on Jan 28, 2010 |
| Title |
negative control inhibitor (NTC1)_24-10 |
| Sample type |
RNA |
| |
|
| Source name |
OVSAYO ovarian cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
protocol: control
|
| Treatment protocol |
Transfection conditions for each clear cell ovarian cancer cell line were optimized for maximum efficiency in preliminary experiments using Dy547-labeled miRIDIAN hairpin inhibitor and mimic transfection controls (Dharmacon). OVSAYO cells were transfected in 6-well plates (3.0 x 105 cells/well) using 3 μl Invitrogen Lipofectamine 2000 and 3 μg total hairpin inhibitor (66 nM). Knockdown of hsa-mir-30 family miRNAs was achieved using a mix of 2 μg hsa-mir-30a inhibitor (44 nM) and 1 μg hsa-mir-30d inhibitor (22 nM). Control groups were cells treated with transfection reagent alone (mock transfection), and cells transfected with miRIDIAN hairpin inhibitor negative control #1 or mimic negative control #2, which are based on C. elegans miRNAs that have minimal sequence identity to human miRNAs (Dharmacon).
|
| Growth protocol |
OVSAYO cells were cultured in RPMI 1640 (Invitrogen), with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin solution (Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested 48 hours after transfection. Total RNA was extracted using the mirVana miRNA Isolation Kit (ABI). RNA quality were inspected on a 2100 Bioanalyzer (Agilent).
|
| Label |
biotin
|
| Label protocol |
According to Illumina protocol.
|
| |
|
| Hybridization protocol |
According to Illumina protocol.
|
| Scan protocol |
According to Illumina protocol.
|
| Description |
negative control inhibitor (mir-30a knockdown control), biological rep1
|
| Data processing |
The image data were compiled into a project using Beadstudio software gene expression module version 3.2.7. No normalization was used. The data was exported as txt files using the build-in function of export to GeneSpring GX format. The option of sample probe profile was chosen. Data were subsequently quantile normalized for the analysis.
|
| |
|
| Submission date |
Jun 12, 2009 |
| Last update date |
Jan 28, 2010 |
| Contact name |
Chad Creighton |
| E-mail(s) |
creighto@bcm.tmc.edu
|
| Organization name |
Baylor College of Medicine
|
| Department |
Biostatistics, Ducan Cancer Center
|
| Street address |
One Baylor Plaza, Mail Stop: BCM305
|
| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
| |
|
| Platform ID |
GPL6947 |
| Series (2) |
| GSE16569 |
Gene expression analyses of mir-30a knockdown in ovarian clear cell cancer cell line |
| GSE16574 |
Gene expression analyses of putative miRNA targets in ovarian clear cell cancer cell lines |
|
