|
| Status |
Public on Feb 27, 2017 |
| Title |
H2009mock3 |
| Sample type |
RNA |
| |
|
| Source name |
NSCLC cell line H2009, mock
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: H2009
cell type: non-small cell lung cancer (NSCLC) cell line
plasmid: empty vector
|
| Treatment protocol |
wtB2M cells were infected with a plasmid carrying B2M gene; mock cells correspond to the infection with the empty vector.
|
| Growth protocol |
Cells grown in HITES with 5% FBS.
|
| 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 Low Input QuickAmp Labeling Kit (Agilent Technologies, Palo Alto, Calif, USA) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).
|
| |
|
| 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 manufacturer's 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.
|
| 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 |
Jun 17, 2016 |
| 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 (1) |
| GSE83490 |
Identification of expression patterns after B2M restoration in deficient lung cancer cell lines |
|
| Relations |
| Reanalyzed by |
GSE113533 |
