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Genes affected by hog1 alleviation of CHS silencing | ||||
| Experiment Name: | Genes affected by hog1 alleviation of CHS silencing | |||
| Accession No. & GeneChip: | AT14, ATH1-121501 | |||
| Submitter: | Experimenter: Nick Jordan, submitted by Lishuang Shen | |||
| Experiment Type: | effect of gene knock-out | |||
| Experiment Factor: | genotype | |||
| Number of Replicates: | 4 | |||
| Quality Control Steps: | biological replicates | |||
| Quality Control Description: | None | |||
| Publication_id: | None | |||
| Last Update Time: | 2004-06-10 09:34:41 | |||
| Expression Data Access & Analysis: | Please select one action: 1. Batch download all data files at Download Center . 2. Browse Hybridizations and boxplots from experiment. 3. Visualization of hybridizations or treatment means with scatterplots and MvA plots. 4. Browse Samples from experiment. 5. Create Gene List by filter probe sets for differentially-expressed genes. 6. Pattern Recognition on filtered gene list. | |||
| Description: | This experiment submission is a courtesy of the Nottingham Arabidopsis Stock Centre's microarray database (http://ssbdjc2.nottingham.ac.uk/narrays/experimentbrowse.pl).The data was generated from NASC's Affymetrix service and offered for public access at BarleyBase. If you publish with this data, please reference data from NASC/GARNet: Craigon DJ., James N., Okyere J., Higgins J., Jotham J., May S. NASCArrays: A repository for Microarray Data generated by NASC's Transcriptomics Service. Nucleic Acids Research, (2004). volume 32, Database issue D575-D577. Following is the original experiment description: About the Experimenter Name: Dr Nick Jordan Head of Lab Name: Dr Ian Furner Address: University of Cambridge Department of Genetics Downing Street Cambridge Postcode: CB2 3EH Country: UK Telephone Number: 01223 333959 Fax Number: 01223 333992 Experiment: Genes affected by hog1 alleviation of CHS silencing Submitted to this database: 27/10/2003 Experiment Description As part of an investigation into mechanisms of HDG silencing in Arabidopsis, we have produced transgenic plants containing extra copies of the chalcone synthase (CHS) gene. The CHS gene mediates an early step in the biosynthesis of the purple pigment anthocyanin. The insertion of extra copies of CHS in Arabidopsis caused the gene to be silenced in some plants. Seeds harvested from these CHS-silenced plants were mutated by treatment with ems. The progeny of these seeds were screened for "revertants" in which the effects of CHS silencing was alleviated and plants were able to produce anthocyanin. These revertants were found to contain a single recessive mutation; the trait has been termed hog1 (for homology dependant gene silencing 1). Our previous experiment used the Affymetrix 8200 chip to make comparisons between gene expression in the two genetic variants: the CHS-silenced type (ECG) and the anthocyanin-producing revertants (15B). Results showed that there were over 100 genes with at least a 10-fold increase or decrease in expression. However, the variation between 2 reps of each genetic variant was high. We would now like to carry out a modified version of this experiment using the 25K Affymetrix chip. It is intended to increase the number of reps to 4, and take samples at an earlier stage than previously in order to decrease the effect of developmental spread. To reduce the effects of interplant variability, samples will be generated from total plant tissue from a pool of 10 plants at GS 1.04. RNA will be purified using RNeasy kits from Qiagen. All of the data available in this website/database is free, and you are free to do whatever you please with it. If you intend to publish work based on any of this data, please acknowledge us, contact the experimenter above, and either acknowledge them or use them as co-authors in the work. About this Experiment Experiment Type: mutant/wildtype Experimental Parameters: parameter mutant/wildtype Quality Control Measures Taken: no-plants-pooled 10, biological-replicates 4 | |||
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