|
| Status |
Public on Jan 31, 2016 |
| Title |
colorectal carcinoma cells with overexpressed TP53 using TAS ChipD |
| 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 TAS.
|
| 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 Tiling Array Software (TAS) using standard parameters according to Kampa et al. ("Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22.". Genome Research, 14:331-42, 2004.). We set bandwith=35, i.e. on average the probe intensities are smoothed by calculating the Hodges-Lehman estimator over 3 probes, and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal length of segments to be reported as highly expressed was set to minrun=90. Perfect match (PM) and mismatch (MM) probe intensities were utilized in using an intensity threshold of 150.
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| |
|
| 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 |
GPL6159 |
| Series (2) |
| GSE29840 |
Expression analysis of colorectal carcinoma cells with overexpressed TP53 using TAS |
| GSE29841 |
Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TAS |
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