|
| Status |
Public on Dec 19, 2018 |
| Title |
CONTROL3 |
| Sample type |
RNA |
| |
|
| Source name |
MIA PaCa-2 after 48h control (DMSO)
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: 48h control (DMSO)
cell line: MIA PaCa-2
cell type: Commercial cell line derived from pancreatic cancer patient.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each condition with RNeasy Mini Kit (Qiagen Iberica) following manufacturer´s instructions. RNA quality and quantity were checked by UV spectroscopy (Nanodrop 2000 Spectrophotometer, Thermo Scientific, Waltham).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Dec 18, 2018 |
| Last update date |
Dec 19, 2018 |
| Contact name |
ROBERTO MARTIN-HERNANDEZ |
| Organization name |
IMDEA ALIMENTACION
|
| Department |
BIOSTATISTICS AND BIOINFORMATICS UNIT
|
| Street address |
CANTOBLANCO
|
| City |
MADRID |
| ZIP/Postal code |
28049 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13607 |
| Series (2) |
| GSE124042 |
Yarrow and marigold extracts and their effect in pancreatic cancer cells [CAL] |
| GSE124044 |
Yarrow and marigold extracts and their effect in pancreatic cancer cells |
|
