|
| Status |
Public on Jan 31, 2016 |
| Title |
colorectal carcinoma cells with overexpressed TP53 using TileShuffle ChipA |
| Sample type |
RNA |
| |
|
| Source name |
Colorectal carcinoma cells with overexpressed TP53
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: colorectal carcinoma cells
treatment: induced expression of 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 overexpressed TP53 on Affymetrix Human Tiling 1.0 array set. TP53 expression has been induced. Expression data was processed with our novel permutation algorithm TileShuffle.
|
| Data processing |
Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. The expression data were processed with our new permutation approach TileShuffle. TileShuffle was applied using only perfect match (PM) probes, a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, three GC content bins, 10000 permutations, and a q-value threshold of 0.05. In order to estimate the significance of a window score we repeatedly permute all probe intensities across the array while interchanging only those that belong to the same sequence-specific affinity bin, recompute the window scores, and compare them with the original ones. By counting the number of permuted windows with higher score, we estimate empirical p-values of windows, and report q-values adjusted according to Benjamini and Hochberg ("Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing". Journal of the Royal Statistical Society. Series B (Methodological), 57:289-300, 1995.).
|
| |
|
| 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) |
| GSE29845 |
Expression analysis of colorectal carcinoma cells with overexpressed TP53 using TileShuffle |
| GSE29970 |
Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TileShuffle |
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