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| 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.).
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| |
|
| 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 |
GPL6161 |
| 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 |
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