|
| Status |
Public on Jan 31, 2016 |
| Title |
colorectal carcinoma cells with defunct TP53 using MAT ChipA |
| Sample type |
RNA |
| |
|
| Source name |
Colorectal carcinoma cells with defunct TP53
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal carcinoma cells
treatment: defunct TP53
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
10µg RNA were analyzed on Affymetrix Human Tiling 1.0 array set according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
Affymetrix Human Tiling 1.0 arrays were proceed using the GCS3000 7G system according to manufacturer's protocol.
|
| Scan protocol |
Affymetrix Human Tiling 1.0 array were proceed using the GCS3000 7G system according to manufacturer's protocol.
|
| Description |
Whole transcriptome expression analysis of colorectal carcinoma cells with defunct TP53 on Affymetrix Human Tiling 1.0 array set. Expression data was processed with MAT.
|
| Data processing |
Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The expression data were processed with MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 1e-5 which yielded the best results from the set of tested parameter values.
|
| |
|
| Submission date |
Jun 08, 2011 |
| Last update date |
Jan 31, 2016 |
| Contact name |
Kristin Reiche |
| E-mail(s) |
kristin.reiche@izi.fraunhofer.de
|
| Organization name |
Fraunhofer Institute for Cell Therapy and Immunology
|
| Department |
Diagnostics
|
| Street address |
Perlickstr. 1
|
| City |
Leipzig |
| ZIP/Postal code |
04103 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6156 |
| Series (2) |
| GSE29829 |
Expression analysis of colorectal carcinoma cells with defunct TP53 using MAT |
| GSE29831 |
Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using MAT |
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