K562 Gene Expression Control vs 1R-Chl treatments
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | C. James Chou
|
| Species: | Homo sapiens |
| Platform: | Affymetrix GeneChip Human Genome U133 Plus 2.0 Array |
| Number of Samples: | 6 |
| Date Range: | 09/07/2006 - 09/07/2006 |
| Experiment Quality: | 98.17 1.37 % |
| Link to Repository: | GSE8832 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | |
| Data Rank: | 
|
To determine whether the polyamide-Chl conjugate 1R-Chl would cause similar changes in global gene expression in K562 cells, affymetrix gene chip analysis was performed using 1R-Chl. Through class comparison analysis, 1R-Chl affected the levels of transcription and genes of interest were determined.
Design: K562 cells were incubated with 1R-Chl (at 250 nM) or in the absence of polyamide, in triplicate for 24 h before RNA purification and microarray analysis at The Scripps Research Institute microarray facility. Affymetrix U133A Plus 2.0 GeneChips were hybridized in groups of three for each of the two groups. The Affymetrix probe set data were imported into BRB Arraytools (3.5.0 Beta 2), selecting the U133 chips used in the experiment and leaving all filters off.
Type: Treatment response
Contents |
[edit] Contributors
- Joel M Gottesfeld
- Peter B Dervan
- James C Chou
- Michelle E Farkas
- Sherry M Tsai
- David A Alvarez
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE8832. (Public on Aug 22 2007)
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| K562_NoTreatmentControl_24hrs_rep1 | 09/07/06 12:43:44 | GSM219392 | 
| 
| 98.0426 0.67 % |
| K562_NoTreatmentControl_24hrs_rep2 | 09/07/06 12:55:17 | GSM219393 | 
| 
| 98.1497 0.39 % |
| K562_NoTreatmentControl_24hrs_rep3 | 09/07/06 13:06:54 | GSM219394 | 
| 
| 98.2572 0.13 % |
| K562_1R-Chl_24hrs_rep1 | 09/07/06 13:18:24 | GSM219395 | 
| 
| 98.2989 0.09 % |
| K562_1R-Chl_24hrs_rep2 | 09/07/06 13:30:03 | GSM219396 | 
| 
| 98.1077 0.76 % |
| K562_1R-Chl_24hrs_rep3 | 09/07/06 13:43:02 | GSM219397 | 
| 
| 98.1835 6.2 % |
