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Beatrice Schildknecht NASC

NASC. Nottingham Arabidopsis Stock Centre http://Arabidopsis.info. Beatrice Schildknecht NASC. Data Availability and NASC tools. Feb 2005. Garnet.arabidopsis.org.uk. NASC. NASC Affy data. NASCArrays is the Affymetrix database for Arabidopsis.

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Beatrice Schildknecht NASC

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  1. NASC Nottingham Arabidopsis Stock Centre http://Arabidopsis.info Beatrice SchildknechtNASC Data Availability and NASC tools Feb 2005 Garnet.arabidopsis.org.uk

  2. NASC NASC Affy data • 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.

  3. 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.

  4. NASC NASC data • 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.

  5. NASC NASCarrays database From Sample to Hybridised Array Labelling protocol Extraction protocol Labelled RNA RNA extract Hybridisation protocol Treatment Hybridised mix Control Affymetrix chip Biological sample Scanning Hybridisation parameters Raw intensity values Adopted from Miller et al, ‘Conforming to MIAME’ www.man.ac.uk

  6. NASC Access data

  7. NASC Browse experiments

  8. NASC Keyword search

  9. NASC Slide search

  10. NASC Get the data

  11. NASC Get the data

  12. NASC The data

  13. 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.

  14. NASC Spot History What is it? • Data mining tool • It shows what a gene does over all slides in the form of a histogram

  15. NASC Spot History

  16. 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.

  17. NASC Gene Swinger Gene has been most variable!

  18. 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.

  19. NASC Two gene scatterplot Click on an outlier Find out which slide has behaved strangely.

  20. NASC Gene Bulk download

  21. NASC Other sources of Data • 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/

  22. NASC

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