|
Status |
Public on Oct 07, 2015 |
Title |
NCI-N417_Scramble8 |
Sample type |
RNA |
|
|
Source name |
Small Cell Lung Cancer (SCLC)
|
Organism |
Homo sapiens |
Characteristics |
cell line: NCI-N417 shRNA: transfected with Scramble 8 (short hairpin RNA number 8 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 8 (short hairpin RNA number 8 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 |