Check out this useful chapter ‘The Caenorhabditis elegans Transgenic Toolbox‘ by Jeremy Nance and Christian Frøkjær-Jensen in the latest issue of WormBook, GENETICS.
New SPELL server: Fresh look and faster
Please note that we have moved the WormBase SPELL tool to a new server on the Amazon Cloud: https://spell.wormbase.org. This should not affect any of our users, as the ‘Tools’ link on the main WormBase menu bar will take you to this new URL.
SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and Proteomics data. Given a small set of query genes, SPELL identifies which datasets are most informative for these genes, then within those datasets, additional genes are identified with expression profiles most similar to the query set. WormBase SPELL has collected over 6,000 experiments for 9 nematode species. Users can also download these datasets for their own analysis. See WormBase SPELL Tutorial: http://wiki.wormbase.org/index.php/SPELL
The new WormBase SPELL server is twice as fast as the old version. Please give it a try and let us know what you think!
Which WB tool to use -check out our updated list and links
If you’re wondering which WormBase tool to use for your data needs, check out this updated list of tools with short descriptions for what to use them for. Click on the tool names to be taken directly to the tool.
Check out SPELL for microarray, tiling array and RNA seq data
SPELL (Serial Pattern of Expression Levels Locator) is a query-driven search engine for microarray, RNAseq and tiling array data. Given a small set of query genes, SPELL can identify which datasets are most informative for these genes, then within these datasets, additional genes are identified with expression profiles most similar to the query set. SPELL contains more than 5000 experiments from over 300 plus datasets.
You can also download datasets by following the ‘Dataset Listing‘ link from the side menu bar on the SPELL home page.
Obtain gene data using SimpleMine
You can query certain types of gene data such as expression in tissue and life stage, RNAi phenotypes, allele phenotypes and gene descriptions using the SimpleMine tool. You can paste in a list of gene names of interest or upload a file with gene names.