|
| Status |
Public on Jun 06, 2012 |
| Title |
Whole transcriptome differential expression analysis of HFF cells using MAT (G0 phase versus G1 phase)_chipD |
| Sample type |
RNA |
| |
|
| Source name |
Human foreskin fibroblasts (HFF) residing in G0 phase compared to HFF cells residing in G1 phase of mitotic cell cycle
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HFF
data processing: MAT
|
| 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 differential expression analysis of HFF cells on Affymetrix Human Tiling 1.0 array set. Cells were synchronised by serum starvation and transcriptome-wide changes occurring at the transition from G0 phase to G1 phase detected. Expression data and fold changes were processed with MAT.
|
| 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 MAT (Johnson et al., "Model-based analysis of tiling-arrays for ChIP-chip." Proc Natl Acad Sci USA, 103:12457-62, 2006.). Parameters for MAT as given in Johnson et al. are geared towards ChIP-chip analysis and, thus, not suitable for expression analysis. Upon inspection of positive control transcripts, we identified optimal parameters for MAT as the same or analogous values as taken for TAS (Tiling Array Software). We set bandwith=35 and the maximal gap between positive probes to be included in a positive interval was set to maxgap=40. The minimal probe count was set to minprobe=3. Only perfect match (PM) probe intensities were utilized. A p-value threshold for expression analyses was set to 5e-2 which yielded the best results from the set of tested parameter values. Differentially expressed segments were identified with the following parameters: We set bandwith=150 and the maximal gap between probes to be included in a differentially expressed interval was set to maxgap=40. The minimal length of differentially expressed segments was set to minprobe=3. Here we use a q-value < 1e-6 which results in an FDR of 17%. To avoid that signal intensity variation at the detection limit is classified as differential expression, we require that differentially expressed intervals must also be significantly expressed in at least one of the investigated conditions, and call these intervals highdiff. Following this definition, we identify highdiff intervals by intersecting intervals identified as differentially expressed with those intervals deemed as 'expressed' in at least one of the compared biological states.
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| |
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| Submission date |
Feb 29, 2012 |
| 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 |
GPL6159 |
| Series (2) |
| GSE36156 |
Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [MAT] |
| GSE36187 |
Differential expression analysis of HFF cells in G0 phase compared to cells in G1 using MAT |
|
| Relations |
| Reanalysis of |
GSM739232 |
| Reanalysis of |
GSM739246 |
