|
| Status |
Public on Jun 06, 2012 |
| Title |
HFF cells using TAS (G1 phase) ChipE |
| 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 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 |
GPL6160 |
| Series (2) |
| GSE29834 |
Expression analysis of HFF cells in G1 phase using TAS |
| GSE36189 |
Differential expression analysis of HFF cells in G0 phase compared to cells in G1 using TAS |
|
| Relations |
| Reanalyzed by |
GSM881904 |
| Reanalyzed by |
GSM882002 |
| Reanalyzed by |
GSM881918 |
| Reanalyzed by |
GSM881968 |
| Reanalyzed by |
GSM882016 |
