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Sample GSM739234 Query DataSets for GSM739234
Status Public on Jun 06, 2012
Title HFF cells using TAS (G0 phase) ChipF
Sample type RNA
 
Source name Human foreskin fibroblasts (HFF) in G0 phase of mitotic cell cycle
Organism Homo sapiens
Characteristics cell line: HFF
phase: G0
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 HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and reside in G0 phase of mitotic cell cycle. 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 Jun 07, 2012
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 GPL6161
Series (2)
GSE29833 Expression analysis of HFF cells in G0 phase using TAS
GSE36189 Differential expression analysis of HFF cells in G0 phase compared to cells in G1 using TAS
Relations
Reanalyzed by GSM881891
Reanalyzed by GSM881989
Reanalyzed by GSM881919
Reanalyzed by GSM881969
Reanalyzed by GSM882017

Supplementary file Size Download File type/resource
GSM739234.CEL.gz 22.6 Mb (ftp)(http) CEL
GSM739234_CC_G0_chipF_NCBIv36_signal_Hs_hg18.bed.gz 35.5 Kb (ftp)(http) BED
Processed data provided as supplementary file
Processed data are available on Series record

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