|
| Status |
Public on Oct 07, 2015 |
| Title |
NCI-N417_Scramble5 |
| Sample type |
RNA |
| |
|
| Source name |
Small Cell Lung Cancer (SCLC)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: NCI-N417
shRNA: transfected with Scramble 5 (short hairpin RNA number 5 doubly mutated)
|
| Treatment protocol |
Not special additional treatment
|
| Growth protocol |
Cells where growth on RPMI media with 10% FBS, 1% PS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extrated using Trizol Reagent.
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 100ng. Commercial One-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90040 of May 2010. Amplification: by RNA polymerases. Briefly, MMLV-RT retrotranscription of sample from a T7 promoter primer is followed by a T7 RNA pol catalysed in vitro transcription reaction in the presence of Cy3-CTP fluorophore. Labeled samples are purified with silica-based spin columns.
|
| |
|
| Hybridization protocol |
Microarray: Human Gene Expression G3 v2 60K (Agilent microarray design ID 039494, P/N G4851B). Microarray sequences and annotations are listed in sheet '039494_hg19_20120628'. Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of labeled extract used: 600 ng. Volume: 50 µL. Temperature (ºC): 65. Duration: 17 hours.
|
| Scan protocol |
Scanned on an G2505C DNA microarray scanner (Agilent).
|
| Description |
NCI-N417 cell line transfected with Scramble 5 (short hairpin RNA number 5 doubly mutated)
|
| Data processing |
Images were analysed by Agilent Feature Extraction Software (ver. 11.5), which performed feature quantitation and additive detrend correction. No background subtraction was performed.
|
| |
|
| Submission date |
Jul 07, 2014 |
| 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) |
| GSE59136 |
Identification of KAT6B signature on KAT6B deficient SCLC cell Lines |
| GSE62775 |
KAT6B gene deletion as a predictive biomarker to Irinotecan response in small cell lung cancer |
|
| Relations |
| Reanalyzed by |
GSE113533 |
