Presentation on theme: "Garnet.arabidopsis.org.uk Beatrice Schildknecht NASC Data Availability and NASC tools NASC Nottingham Arabidopsis Stock Centre"— Presentation transcript:
Garnet.arabidopsis.org.uk Beatrice Schildknecht NASC Data Availability and NASC tools NASC Nottingham Arabidopsis Stock Centre http://Arabidopsis.info Feb 2005
NASCArrays is the Affymetrix database for Arabidopsis. 1567 chips (in 91 experiments) are available for download. All experiments samples are fully annotated (MIAME). All of the data in NASCArrays is free, and you are free to do anything you like with it. NASC NASC Affy data
http://affymetrix.arabidopsis.info Or more simply… affy.arabidopsis.info All of our data is available via our NASCArrays website: NASC The NASC Affy website You can download all of the data in the database for use with spreadsheets or microarray analysis packages. Data is also available through some data mining tools, such as spot history.
Since 2002, NASC has operated an Affymetrix service for customers. Our focus is on plant experiments, however we have processed Affymetrix hybridisations for a range of species. Included in the service are all steps after the initial RNA extraction. You: –grow your plants, extract the RNA, and send it to us. We: – QC your sample before proceeding with the sample preparation and hybridization. NASC NASC data
From Sample to Hybridised Array Biological sample Control RNA extract Extraction protocol Treatment Affymetrix chip Hybridisation parameters Hybridised mix Hybridisation protocol Labelled RNA Labelling protocol Adopted from Miller et al, Conforming to MIAME www.man.ac.uk Scanning Raw intensity values NASC NASCarrays database
NASC NASC Tools Spot History: –Look at how your gene has performed over all experiments as a histogram Gene Swinger: –Shows experiments where your gene has been highly variable Two Gene Scatter Plot: –Allows you to see how two genes performed together over all experiments Bulk Gene Download: –Allows you download a selection of genes over several experiments What is it? How to use it.
NASC Spot History What is it? Data mining tool It shows what a gene does over all slides in the form of a histogram
NASC Gene Swinger What is it? Data mining tool Allows you to find interesting experiments for a gene. It shows you experiments where the gene you choose is highly variable, over all the experiments in the database.
NASC Two gene scatterplot What is it? Data mining tool for finding interesting experiments for genes of interest. It shows experiments where genes chosen are highly variable, over all the experiments in the database. Shows if genes are correlated in any way. It also allows you to pick slides that are different from the general trend. This tool plots a scatter plot of the two genes you select over all experiments. Every point on the graph represents one slide.
NASC Two gene scatterplot Click on an outlier Find out which slide has behaved strangely.
ArrayExpress http://www.ebi.ac.uk/arrayexpress/ TAIR http://arabidopsis.org/info/expression/index.jsp Genevestigator https://www.genevestigator.ethz.ch/ AT arrays http://atarrays.tigr.org/arabdata.shtml BarleyBase http:/www.barleybase.org/ NASC Other sources of Data