|
| Status |
Public on Jul 24, 2010 |
| Title |
arpe cells_treated-rep1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
ARPE cells
|
| Organism |
Homo sapiens |
| Characteristics |
agent: control
|
| Treatment protocol |
Treated cells were exposed to 100 uM PDTC (pyrrolidine dithiocarbamate) for 24 h.
|
| Growth protocol |
Cells were grown until semi-confulent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagaent. Small RNA was enriched.
|
| Label |
A3
|
| Label protocol |
PolyA-tailed miRNA was labeled with Alexa Fluor 3 (A3) or Alexa Fluor5 (A50 using the Ncode miRNA labeling system (Cat # 25-0888).
|
| |
|
| Channel 2 |
| Source name |
ARPE cells
|
| Organism |
Homo sapiens |
| Characteristics |
agent: PDTC
|
| Treatment protocol |
Treated cells were exposed to 100 uM PDTC (pyrrolidine dithiocarbamate) for 24 h.
|
| Growth protocol |
Cells were grown until semi-confulent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using TRIzol reagaent. Small RNA was enriched.
|
| Label |
A5
|
| Label protocol |
PolyA-tailed miRNA was labeled with Alexa Fluor 3 (A3) or Alexa Fluor5 (A50 using the Ncode miRNA labeling system (Cat # 25-0888).
|
| |
|
| |
| Hybridization protocol |
MiRNAs were incubated with hubridization solution at 75-80 degrees C for 10 min athen loaded onto array. Arrays were mounted with Maui Mixer SL and hybridized overnight (16-20 h) at 52 degrees C withy conwtant mixing.
|
| Scan protocol |
Arrays were scanned using a GenePix 4000B microarray scanner (Molecular Devices).
|
| Description |
ARPE cells treated with PDTC are c ompared with untreated cells.
|
| Data processing |
The scanned array images were annotated and analyzed using the GenePix® software and the .GAL file containing the array list (NCode™_Multi_Species_20141.GAL). The data output file is saved as a .Gpr file and exported as a .Txt file. The .Txt files were transferred to individual worksheets in a Summary Excel file, individually sorted by name for easy access and analysis using Microsoft Excel.
Blanks, empty spots and dye markers have been removed in all worksheets. The array data were checked to ensure the mean backgrounds were below 50 for both the A3 and A5 channels. The results were also checked for the presence of signal for the NCode™ Multi-Species miRNA Microarray Controls for both the A3 and A5 channels. The experiment passed internal QC specifications for N-Code™ microRNA expression profiling.
Stataistical analysis performed using algorithms in Microsoft Excel to determine mean, std dev. Etc.
|
| |
|
| Submission date |
Jul 23, 2010 |
| Last update date |
Jul 23, 2010 |
| Contact name |
Cynthia Jawoski |
| Organization name |
NIH
|
| Department |
NEI
|
| Lab |
LRCMB
|
| Street address |
bldg 6, room 136
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL10724 |
| Series (1) |
| GSE23107 |
MicroRNA expression from ARPE-19 cells: control and PDTC treated. |
|
