|
| Status |
Public on Mar 14, 2012 |
| Title |
miR-NC_1 |
| Sample type |
RNA |
| |
|
| Source name |
Human pancreatic cancer cells, MIA PaCa-2, transfected with a negative precursor miRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: pancreatic cancer cells
cell line: MIA PaCa-2
transfectant: negative precursor miRNA
|
| Treatment protocol |
Cells were seeded at 2×105/well in 6-well plate and transfected with precursor of miR-193b or with negative controlprecursor (Life technologies) at 30 nM using siPORT NeoFX (Life Technologies) according to the manufacturer’s instructions.
|
| Growth protocol |
Human pancreatic cancer cell line, MIA PaCa-2, cultured with DMEM supplemented with 10% fetal bovine serum at 37˚C in 5% CO2 with appropriate humidity
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using mirVana miRNA Isoraion Kit (Life technologies) according to manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
cRNAs labeled with Cyanin 3 were synthesized by the T7-liner amplification method from 500 ng of the total RNAs employing Low RNA Input Linear Amplification Kit (Agilent Technologies, Palo Alto, CA) and purified using RNeasy mini kit (Qiagen).
|
| |
|
| Hybridization protocol |
1.65 µg of cRNAs were fragmented at 60 ˚C for 30 minutes using Gene Expression Hybridization Kit (Agilent Technologies) and hybridized at 65 ˚C for 17 hours to the 4×44K Whole Human Genome Microarray slide containing 45,015 features representing 41,000 unique probes (Catalog # G4112F, Agilent Technologies) by the method of the manufacturer’s instructions, including 2 biological replications.
|
| Scan protocol |
Microarrays were scanned using Agilent Array Scanner (Agilent technologies). Reproducibility and reliability of each single microarray was assessed using Quality Control report data which were extracted with Agilent feature extraction software (version 10.5.1.1) using the GE1-v5_10_Apr08 protocol.
|
| Description |
Gene expression 48 hours after transfection of a negative precursor miRNA
|
| Data processing |
Data processing was conducted using GeneSpring GX 10.0 software (Agilent Technologies). Expression levels were normalized to the 75 percentile, and baseline transformations were conducted employing the median of control samples in each cell line. Genes whose expressions altered more than 2.5-folds or higher with statistical significance (P < 0.05) in cells transfected with a negative precursor miRNA compated to those transfected with the precursor of miR-193b were listed. Fold change results are available on the Series record (IKEDA_data.txt)
gProcessedSignal data provided by Agilent feature extraction software
|
| |
|
| Submission date |
Nov 09, 2010 |
| Last update date |
Mar 14, 2012 |
| Contact name |
Toru Furukawa |
| E-mail(s) |
toru.furukawa@twmu.ac.jp
|
| Phone |
+81-3-3353-8111
|
| Fax |
+81-3-5269-7667
|
| Organization name |
Tokyo Women's Medical University
|
| Department |
Institute for Integrated Medical Sciences
|
| Street address |
8-1 Kawadacho, Shinjuku-ku
|
| City |
Tokyo |
| ZIP/Postal code |
162-8666 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6480 |
| Series (1) |
| GSE25215 |
Identification of target genes of miR-193b |
|
