|
| Status |
Public on Sep 08, 2016 |
| Title |
H460_shBRG1_COMB_3 |
| Sample type |
RNA |
| |
|
| Source name |
Lung
|
| Organism |
Homo sapiens |
| Characteristics |
individual: Diseased donor
cell line: NSCLC cell line H460
cell line type: MYC amplified
treatment: shBRG1_COMB
|
| Treatment protocol |
GCRA: Dexamethasone (1uM) + Retinoic Acid (1uM) 120hours; COMB: Dexamethasone (1uM) + Retinoic Acid (1uM) + Aza (0.2uM) + SAHA (0.2uM) 120 hours
|
| Growth protocol |
Cells where growth on RPMI media with 10% FBS, 1% PS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using Trizol Reagent.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 45ng total RNA using a LowInput QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a total volume of 25ul following the manufacturers instructions. On completion of the fragmentation reaction, 25ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4851A) 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 |
Scanner Agilent G2565CA Feature extraction 10.7
|
| Description |
Sample name: H460_Sh_COMB_2233
Cancer cell line
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software (Agilent). Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Feb 24, 2015 |
| Last update date |
Apr 23, 2018 |
| Contact name |
Manel Esteller |
| Organization name |
IDIBELL
|
| Department |
PEBC
|
| Lab |
Cancer Epigenetics
|
| Street address |
Hospital Duran i Reynals Av. Gran Via s/n km, 2.7
|
| City |
L'Hospitalet de Llobregat |
| State/province |
Barcelona |
| ZIP/Postal code |
08908 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17077 |
| Series (2) |
| GSE66244 |
Identification of expresion patterns after treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines |
| GSE66245 |
Treatment with GC/RA and combination with AZA/SAHA in MYC amplified and BRG1 mutant lung cancer cell lines |
|
| Relations |
| Reanalyzed by |
GSE113533 |
