|
| Status |
Public on May 30, 2014 |
| Title |
Y79 cells_normal culture_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
Y79 cells, normal culture, 24 hours
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Y79 cell line
|
| Treatment protocol |
No additional treatment was performed other than normal culture conditions. Cells were prepared when they reached the concentration of 5 x 10^5 cells/mL.
|
| Growth protocol |
Y79 cells were maintained in RPMI-1640 media supplemented with 10% fetal bovine serum and 1% (v/v) penicillin-streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent (Invitrogen, Carlsbad, CA).
|
| Label |
Cy3
|
| Label protocol |
For control and test RNAs, the synthesis of target miRNA probes and hybridization were performed using Agilent’s miRNA Labeling Reagent and Hybridization kit (Agilent Technology, USA) according to the manufacturer’s instructions. Briefly, each 100 ng of total RNA were dephosphorylated with ~15 Units of calf intestine alkaline phosphatase (CIP), followed by RNA denaturation with ~40% DMSO and 10 min incubation at 100 °C. Dephosphorylated RNA were ligated with pCp-Cy3 mononucleotide and purified with MicroBioSpin 6 columns (Bio-rad, USA).
|
| |
|
| Hybridization protocol |
After purification, labeled samples were resuspended with Gene Expression blocking Reagent and Hi-RPM Hybridization buffer, followed by boiling for 5 min at 100 °C and 5 min chilled on ice. Finally, denatured labeled probes were pipetted onto assembled Agilent’s miRNA Microarray and hybridized for 20 hours at 55°C with 20 RPM rotating in Agilent Hybridization oven (Agilent Technology, USA).
|
| Scan protocol |
The hybridized images were scanned using Agilent’s DNA microarray scanner and quantified with Feature Extraction Software (Agilent Technology, Palo Alto, CA).
|
| Description |
miRNA
|
| Data processing |
All data normalization and further analysis were performed using Genowiz 4.0TM (Ocimum Biosolutions, India)
|
| |
|
| Submission date |
May 29, 2014 |
| Last update date |
May 30, 2014 |
| Contact name |
Jeong Hun Kim |
| Organization name |
Seoul National University
|
| Lab |
FARB (Fight against Angiogenesis-Related Blindness) Laboratory
|
| Street address |
101, Daehak-ro, Jongno-gu
|
| City |
Seoul |
| ZIP/Postal code |
110744 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL18402 |
| Series (1) |
| GSE58092 |
Investigation of miRNA expression patterns in Y79 cells |
|
