|
| Status |
Public on Nov 15, 2013 |
| Title |
DMS273-DyeSwap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
DMS-273 Control
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: scrambled
cell line: DMS-273 SCLC
tissue: Lung
|
| Growth protocol |
Total RNA fraction. RNA Integrity Numbers were in the range 9.3 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
Cy5
|
| Label protocol |
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 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 either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
Pooled clone 21-30-31 DMS-273
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: SETDB1 KD
cell line: DMS-273 SCLC
tissue: Lung
|
| Growth protocol |
Total RNA fraction. RNA Integrity Numbers were in the range 9.3 to 10.0 when assayed by Lab-chip technology on an Agilent 2100 Bioanalyzer.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol
|
| Label |
Cy3
|
| Label protocol |
Amount of nucleic acid labeled: 100ng. Commercial Two-Color Microarray-Based Gene Expression Analysis (Low Input Quick Amp Labeling) version 6.5 kit by following manufacturer instructions. Agilent manual G4140-90050 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 either Cy3-CTP or Cy5-CTP fluorophores. Labeled samples are purified with silica-based RNeasy spin columns (Qiagen).
|
| |
|
| |
| Hybridization protocol |
Hybridization chamber type: SureHyb hybridization chamber (Agilent). Quantity of each labeled extract used: 300 ng. Volume: 50 uL. Temperature (ºC): 65. Duration: 17 hours.
|
| Scan protocol |
Scanned on an G2505C DNA microarray scanner (Agilent). Images were analysed by Agilent Feature Extraction Software (ver. 10.7), which performed feature quantitation and additive detrend correction. No background subtraction was performed.
|
| Description |
Pooled clone 21-30-31 DMS-273
|
| Data processing |
Data from hybridised microarray images were quantitated, corrected by additive detrending and submitted to dye bias normalisation after bias detection by linear and Lowess curve fitting methods (Agilent FeatureExtraction (FE) Software).Raw data signals are thresholded to 1, and replicated probe signals for the individual channels (Cy5 and Cy3) are summarized by computing their geometric mean. Normalised signal values are obtained by Cy5/Cy3 ratio computing and Log base2 transformation. These manipulations are done with GeneSpring GX12 software.
|
| |
|
| Submission date |
Mar 14, 2013 |
| 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) |
| GSE45175 |
Human lung cancer cell lines DMS-273 (SCLC) and NCI-H1437 (NSCLC): scrambled vs. shRNA clones |
|
| Relations |
| Reanalyzed by |
GSE113533 |
