For our first installment of DAWG in spring 2019, our group leaders are working with Dr. Bert Eardley to analyze his ITS pyrosequences. Dr. Eardley collected and processed samples for ectomycorrhizal (EMF) identification from pitch pines downwind of Zn smelters in Pennsylvania. Our group leaders are working with Dr. Eardley to answer the following questions regarding the EMF ITS sequences:
How are the EMF assemblages different between the pitch pine seedling roots that were treated with inoculant vs the ones that are natural?
How might the metals in the soils be driving community level differences?
How do the EMF assemblages in roots from soil that has naturally high levels of metals (serpentine soil) compare to the EMF assemblages in roots from soils that were down-wind of the Zn smelters?
Since these were pyrosequenced, the output from sequencing is a .sff file. To process the samples, we are using DADA2, which requires demultiplexed .fastq files. Both the demultiplexed .fastq files and the .sff file can be found here:
https://psu.box.com/s/g1gm2ubufj2qevgvo2pfdxfd7djbj6ay
Here is a link to the video of our second DAWG session: https://psu.mediaspace.kaltura.com/media/DAWG+02/1_yu0sk7i9