Week 10 was the last week of class (that’s a quarter system for all semester-types out there).  In the previous class the students got together in groups and produced “consensus” genome announcements for their groups.   In the intervening week, Ashley and I produced a “consensus consensus” Genome Announcement, taking pieces from the various groups.    Then …

The blog posts for the previous 8 weeks were written as group assignments by the students taking this “Swabs to Genomes” class.  For the final two weeks of the quarter, I will just briefly describe what we did on those days. Based on the results from Phylosift, A5-miseq, and RAST we made a call at …

(this blog post was written by group #4 as a writing assignment) Our goal for this week’s lesson was to double check that the genome we sequenced is, in fact, the organism we are interested in. After uploading our sequences up to RAST last week, we found out the results and were able to look …

(this blog post was written by group #3 as a writing assignment) Last week in class we were introduced to genome assembly and validation by using an open-source bacterial genome assembly program A5-miseq. This program produces high quality genome assemblies by automating processes such data processing, error correction, contig and scaffold assembly, and final verification. …

(This post was written by group #2 as a writing assignment) Since we were about half way through this quarter, the activity we did this past week was to summarize all the experiments we have performed so far, list the consumable materials that were used, and any questions or concerns that may have arisen during …

(This blog post was written by group #1 as a writing assignment.  See their first post here.  Note that much of what the students did in this class is taken directly from the Swabs to Genomes paper which contains relevant links and references) This week in class, our goal was to create a phylogenetic tree …

(this post was written by group #4 as a writing assignment) With a minor setback from last week’s inability to efficiently wash and quantify the amplified DNA, we came back this week with a stronger mindset to pick ourselves back up and turn our failures into a positive. At the start of this week’s class, …

(this post was written by group #3 as a writing assignment) After last week, our extracted DNA samples were amplified with PCR and the finished product brought this week to lab for us to purify and prepare for Sanger sequencing. The first step we took this week was to analyze the success of PCR using …

(this post was written by group #2 as a writing assignment) The goal of this week experiment was to extract genomic DNA from our samples for sequencing. Ultimately, we want to characterize the DNA from samples by sequencing them. However, since our isolates are in small amounts, we need to do an additional step (in …

(This post was written by group#1 as a writing assignment) A new class yet to be named begins giving students hands on experience with genomic sequencing. We are attempting to sequence bacteria from diseased abalone. We had fecal samples from both healthy and diseased red abalone and white abalone, 4 in total. In the first …