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Status |
Public on Jan 15, 2007 |
Title |
A549, let-7-a3, overexpression, Replicate 4 |
Sample type |
RNA |
|
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Channel 1 |
Source name |
P324 cell line A549
|
Organism |
Homo sapiens |
Characteristics |
cell line A549, control
|
Biomaterial provider |
Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
|
Treatment protocol |
non-treated
|
Growth protocol |
cells were cultivated in DMEM medium supplemented with 10% FCS
|
Extracted molecule |
total RNA |
Extraction protocol |
total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)
|
Label |
Cy3
|
Label protocol |
direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy3-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy3-labeled probes were purified with Microcon YM-30 column.
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|
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Channel 2 |
Source name |
P320 cell line A549
|
Organism |
Homo sapiens |
Characteristics |
cell line A549, let-7-a3, stable transfection
|
Biomaterial provider |
Division of Epigenetics, German Cancer Research Center, Heidelberg, Germany
|
Treatment protocol |
non-treated
|
Growth protocol |
cells were cultivated in DMEM medium supplemented with 10% FCS
|
Extracted molecule |
total RNA |
Extraction protocol |
total RNA was extracted using Qiagen RNeasy Midi Kit reagents; 2µg total RNA was amplified one round based on T7 RNA Polymerase (Agilent low RNA Input Amplification Kit)
|
Label |
Cy5
|
Label protocol |
direct fluorescent labelling of 2 µg amplified RNA, anneling of 0.5µg Random Primer and reverse-transcribed into cDNA with Superscript III reverse transcriptase for 1h at 42°C in the presence of 0.4 mM dGTP, 0.4 mM dATP, 0.4 mM dTTP, 0.24 mM dCTP, 0.125 mM Cy5-dCTP. After hydrolysis of RNA in 0.2 M NaOH, Cy5-labeled probes were purified with Microcon YM-30 column.
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|
|
Hybridization protocol |
ch1 and ch2 together are solved in 50 µl 1x DIG-Easy hybridization buffer (Roche Diagnostics, Mannheim, Germany), containing 10x Denhardt’s solution and 2 ng/µl Cot1-DNA (Invitrogen); sample was denaturated at 65°C for 2min, hybridzation of arrays were performed in Corning chambers 14h at 37°C; slides were washed twice in 1xSSC+0.1SDS and once in 0.1xSSC+ 0.1SDS before air pressure drying and scanning.
|
Scan protocol |
arrays were scanned with the GenePix 4000B microarray scanner and analyzed using GenePix Pro 4.1 software (Axon Instruments)
|
Description |
A549, let-7-a3, overexpression, Replicate 4
|
Data processing |
raw data processing was performed using ArrayMagic (Buness et al., 2005) and VSN normalization method; after removal of bad quality clones, generalized log ratios from 26629 cDNA clones were given in the data table
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Submission date |
Dec 06, 2006 |
Last update date |
Dec 08, 2006 |
Contact name |
Ruprecht Kuner |
Organization name |
German Cancer Research Center and National Center of Tumor Diseases
|
Department |
Molecular Genetics
|
Lab |
Unit Cancer Genome Research
|
Street address |
Im Neuenheimer Feld 460
|
City |
Heidelberg |
ZIP/Postal code |
69120 |
Country |
Germany |
|
|
Platform ID |
GPL3050 |
Series (1) |
GSE6474 |
miRNA let-7a-3 overexpression in lung cancer cell line A549 |
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