|
| Status |
Public on Dec 17, 2014 |
| Title |
KB 1h PD98059 1h IL1a / KB 1h IL1a _rep2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Human epithelial KB cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KB
treatment: 1h PD98059 1h IL1a
|
| Treatment protocol |
An individual set of samples was treated identically with IL1a but after an initial preincubation for 1h with PD98059 (50 micromol/l). Each dual-color microarray represents a direct comparison of samples preincubated or not with PD98059.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA utilized for microarray experiments was prepared with NucleoSpin RNA Kit (#740955.50, Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations.
|
| Label |
Cy3
|
| Label protocol |
cRNA synthesis was performed with the ‘Low RNA Input Linear Amplification Kit PLUS Two-Color’ (#5188-5340, Agilent Technologies).
|
| |
|
| Channel 2 |
| Source name |
Human epithelial KB cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: KB
treatment: KB 1h IL1a _rep2
|
| Treatment protocol |
An individual set of samples was treated identically with IL1a but after an initial preincubation for 1h with PD98059 (50 micromol/l). Each dual-color microarray represents a direct comparison of samples preincubated or not with PD98059.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA utilized for microarray experiments was prepared with NucleoSpin RNA Kit (#740955.50, Macherey-Nagel, Düren, Germany) according to the manufacturer’s recommendations.
|
| Label |
Cy5
|
| Label protocol |
cRNA synthesis was performed with the ‘Low RNA Input Linear Amplification Kit PLUS Two-Color’ (#5188-5340, Agilent Technologies).
|
| |
|
| |
| Hybridization protocol |
cRNA synthesis, cRNA fragmentation, hybridization and washing was carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol’ V5.0.1(Agilent Technologies), except that 5µg of labeled cRNA were used for hybridization.
|
| Scan protocol |
Slides were scanned on an Agilent Microarray Scanner G2505B in extended dynamic range mode at two PMT settings (100 % and 5 %) to increase the dynamic range of the measurements.
|
| Data processing |
Data extraction was performed with the ‘Feature Extraction Software’ V9.5.3.1 by using the default extraction protocol files ‘GE2-v5_95_Feb07.xml’.
|
| |
|
| Submission date |
Dec 16, 2014 |
| Last update date |
Dec 17, 2014 |
| Contact name |
Marek Bartkuhn |
| E-mail(s) |
marek.bartkuhn@gen.bio.uni-giessen.de
|
| Organization name |
Justus-Liebig-University Giessen
|
| Department |
Biomedical Informatics and Systems Medicine
|
| Street address |
Aulweg 132
|
| City |
Giessen |
| State/province |
Hessen |
| ZIP/Postal code |
35392 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4133 |
| Series (2) |
| GSE64224 |
The activation of IL-1 induced enhancers depends on TAK1 kinase activity and NF-KB p65 |
| GSE64237 |
The activation of IL-1-induced enhancers depends on TAK1 kinase activity and NF-kappaB p65 II |
|
