|
| Status |
Public on Jun 06, 2012 |
| Title |
Whole transcriptome differential expression analysis of HFF cells using TAS (G0 phase versus G1 phase)_chipH |
| 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: TAS
|
| 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 TAS.
|
| Data processing |
Affymetrix Human Tiling 1.0 probes were mapped to human genome assembly hg18 using corresponding BPMAP files. The 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.). In order to identify highly expressed segments 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. Differentially expressed segments were identified with the following parameters: Signal intensities of chips of the same type were normalized across the two different biological conditions and log fold changes were calculated. 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 minrun=90. Here we use a q-value < 0.05 which results in an FDR of 18%. 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.
|
| |
|
| 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 |
GPL6163 |
| Series (2) |
| GSE36160 |
Differential expression analysis of HFF cells in G0 phase compared to cells in G1 [TAS] |
| GSE36189 |
Differential expression analysis of HFF cells in G0 phase compared to cells in G1 using TAS |
|
| Relations |
| Reanalysis of |
GSM739236 |
| Reanalysis of |
GSM739250 |
