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Sample GSM739322 Query DataSets for GSM739322
Status Public on Jan 31, 2016
Title colorectal carcinoma cells with defunct TP53 using TAS 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 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.
 
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)
GSE29839 Expression analysis of colorectal carcinoma cells with defunct TP53 using TAS
GSE29841 Differential expression analysis of colorectal carcinoma cells (defunct TP53 versus active TP53) using TAS

Supplementary file Size Download File type/resource
GSM739322.CEL.gz 22.6 Mb (ftp)(http) CEL
GSM739322_KE_nor_chipJ_NCBIv36_signal_Hs_hg18.bed.gz 46.2 Kb (ftp)(http) BED
Processed data are available on Series record
Processed data provided as supplementary file

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