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Sample GSM1088075 Query DataSets for GSM1088075
Status Public on Feb 04, 2014
Title Whole transcriptome analysis of HFF cells using TileShuffle (G1 phase)
Sample type RNA
 
Source name Human foreskin fibroblasts (HFF) in G1 phase of mitotic cell cycle
Organism Homo sapiens
Characteristics cell line: HFF
phase: G1
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 G1 phase of mitotic cell cycle. Expression intensities were processed with TileShuffle.
Data processing Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using the corresponding BPMAP files. Intensities of perfect match (PM) probes were processed with TileShuffle (Otto C, Reiche K, Hackermüller J. "Detection of differentially expressed segments in tiling array data". Bioinformatics. 2012 Jun 1;28(11):1471-9. Epub 2012 Apr 6.) using a window size of 200, the arithmetic mean trimmed by maximal and minimal value as scoring function, four 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 Feb 25, 2013
Last update date Feb 05, 2014
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 GPL6163
Series (3)
GSE44628 Expression analysis of HFF cells in G1 phase
GSE44631 Differential expression analysis of HFF cells in G0 phase compared to cells in G1
GSE44632 Differential expression analysis of HFF cells in G1 phase compared to cells in S

Supplementary file Size Download File type/resource
GSM1088075_CC_G1_chipH.CEL.gz 23.7 Mb (ftp)(http) CEL
GSM1088075_CC_G1_chipH_high.bed.gz 68.9 Kb (ftp)(http) BED
Processed data provided as supplementary file

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