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Sample GSM739421 Query DataSets for GSM739421
Status Public on Jan 31, 2016
Title colorectal carcinoma cells with defunct TP53 using TileShuffle ChipJ
Sample type RNA
 
Source name Colorectal carcinoma cells with defunct TP53
Organism Homo sapiens
Characteristics cell type: colorectal carcinoma cells
treatment: with 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 our novel permutation approach 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 GPL6165
Series (2)
GSE29844 Expression analysis of colorectal carcinoma cells with defunct TP53 using TileShuffle
GSE29970 Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TileShuffle

Supplementary file Size Download File type/resource
GSM739421.CEL.gz 22.6 Mb (ftp)(http) CEL
GSM739421_KE_nor_chipJ_high_a.bed.gz 92.9 Kb (ftp)(http) BED
Processed data provided as supplementary file

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