Following is an early work-in-progress draft for an upcoming zine “Genome assembly for artists.” The content here is released under CC BY-NC-SA license. Normally I work with publicly accessible databases full of assembled genomes and other biological data, like the almost eponymous NCBI Genbank.
Quick note on what might be a second-to-last test of the HMW Deinococcus genome extraction. I set up a 24 hour ethanol precipitation reaction following the usual lysis step.
Continuing on with optimizing the Deinococcus genome extraction for long-read sequencing.
The surprisingly eventful high molecular weight genome extraction tests for the new Deinococcus species continues. All this is a bit of a pain point inherent in self-funded amateur research, since purchasing specialty kits for different lab processes needs to be avoided whenever possible, both for sake of knowledge and for financial restraints.
Tonight marks the completion of our third Deinococcus genome extraction test. First two processes were adopted from my Halobacterium protocol – alas, they were both subpar compared to the Deinococcus radiophilus genome extract we made two years ago.
Noting an interesting observation on culturing the new Deinococcus species in the lab. I’ve been running some tests regarding growth conditions of the new Deinococcus species, and am pretty confident the particular species grows far better under room temperature conditions, as far as liquid cultures are concerned.
Lots of little maintenance activities today: None of the later inoculations of the recent Deinococcus acquisition show the weird clumping behavior seen in the first flask, documented on previous post. At this time I’m almost certain that the clumping behavior in liquid culture was a contamination from the sponge topper for the flask.
Just a quick post for record’s sake. Initial liquid culture inoculation made on the 9th seems oddly slow, and displays clumping in the flask.
The new Deinococcus species we received for a collaboration grew on our TGYM media without any issues. New plates were struck out on October 6th, and colonies formed by early October 8th, somewhat less than two day turnaround in line with our experience with Deinococcus radiophilus.
Quick lab note update for today’s new arrival. Our small amateur biology lab’s microscopic zoo continues to grow in size- some plates and agar stabs of a new Deinococcus species (to us) just arrived from our collaborator’s lab, along with a fresh rapid sequencing kit for round two of rapid long-read sequencing experiment.
It’s been a while since the last lab note update – August 26th post on Halobacterium genome extraction was the last post, more than a month ago.
