Expression data from leaf of Arabidopsis TGS mutants
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | Yoshiki Habu habu@affrc.go.jp |
| Species: | Arabidopsis thaliana |
| Platform: | Affymetrix GeneChip Arabidopsis 8k |
| Number of Samples: | 5 |
| Date Range: | 01/19/2001 - 01/24/2001 |
| Experiment Quality: | 97.56 3.48 % |
| Link to Repository: | GSE5771 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | platform not found in Bioconductor |
| Clean PLIER Data: | platform not found in Bioconductor |
| Clean CEL Files: | Download |
| Data Rank: | 
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Transcriptional gene silencing (TGS) in Arabidopsis is regulated by two distinct pathways, DNA methylation-dependent and –independent. ddm1 and mom1 mutants are defective in the DNA-dependent and –independent pathway, respectively.
We used microarrays to detail the global changes in gene expression in the TGS mutants
Design: We sought to obtain differential gene expression in each mutant in order to characterize the effect of deficiency in two distinct TGS pathways. To that end, we took mutants that regulate TGS by DNA methylation-dependent (ddm1) and -independent (mom1) pathways, respectively. Total RNA was extracted from leaves of these mutants and subjected to hybridization on Affymetrix Arabidopsis 8K microarrays.
Type: TGS mutants
Contents |
[edit] Contributors
- Jerzy Paszkowski
- Tong Zhu
- Yoshiki Habu
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE5771. (Public on Aug 29 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 |
|---|---|---|---|---|---|
| Zurich_leaf | 01/24/01 12:10:54 | GSM134890 | 
| 
| 95.0474 7.56 % |
| LineA_leaf | 01/19/01 14:26:16 | GSM134891 | 
| 
| 97.743 2.25 % |
| mom1-1_leaf | 01/19/01 14:04:11 | GSM134892 | 
| 
| 97.2401 2.35 % |
| mom1-1_noHPT_leaf | 01/19/01 13:20:25 | GSM134893 | 
| 
| 98.8422 0.99 % |
| ddm1-5_leaf | 01/19/01 13:53:04 | GSM134894 | 
| 
| 98.913 4.24 % |
