After filtration, all DNA should present in the filter, so we cut the paper up with scissors and put the pieces into an Eppendorf: <video Cutting vacuum pump filter and placing it in Eppendorf>{full}.

\Video[https://upload.wikimedia.org/wikipedia/commons/transcoded/8/85/Vacuum_pump_filter_cut_and_place_in_eppendorf.webm/Vacuum_pump_filter_cut_and_place_in_eppendorf.webm.480p.vp9.webm]
{title=Cutting vacuum pump filter and placing it in <Eppendorf>}
{height=400}

Now that we had the DNA in Eppendorfs, we were ready to continue the purification in a simpler and more standardized lab pipeline fashion.

First we added some small specialized beads and chemicals to the water and shook them Eppendorfs hard in a <Scientific Industries Inc. Vortex-Genie 2> machine to break the <cell (biology)> and free the DNA.

\Video[https://upload.wikimedia.org/wikipedia/commons/transcoded/e/e1/Scientific_Industries_Inc_Vortex-Genie_2_loading.webm/Scientific_Industries_Inc_Vortex-Genie_2_loading.webm.480p.vp9.webm]

\Video[https://upload.wikimedia.org/wikipedia/commons/transcoded/1/19/Scientific_Industries_Inc_Vortex-Genie_2_running.ogv/Scientific_Industries_Inc_Vortex-Genie_2_running.ogv.480p.vp9.webm]
{height=400}

Once that was done, we added several reagents which split the solution into two phases: one containing the DNA and the other not. We would then pipette the phase with the DNA out to the next Eppendorf, and continue the process.

In one step for example, the DNA was present as a white precipitate at the bottom of the tube, and we threw away the supernatant liquid: <image White precipitate formed with Qiagen DNeasy PowerWater Kit>{full}.

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/3/30/Qiagen_DNeasy_PowerWater_Kit_White_Precipitate.jpg/586px-Qiagen_DNeasy_PowerWater_Kit_White_Precipitate.jpg]
{title=White precipitate formed with Qiagen DNeasy PowerWater Kit}

At various stages, centrifuging was also necessary. Much like the previous vacuum pump step, this adds extra gravity to speed up the separation of phases with different molecular masses.

In our case, we used a <VWR Micro Star 17 microcentrifuge> for those steps:

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/0/03/VWR_Micro_Star_17_microcentrifuge.jpg/360px-VWR_Micro_Star_17_microcentrifuge.jpg]
{height=400}
{titleFromSrc}

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/6/65/VWR_Micro_Star_17_microcentrifuge_loading.png/358px-VWR_Micro_Star_17_microcentrifuge_loading.png]
{titleFromSrc}

Then, when we had finally finished all the purification steps, we measured the quantity of DNA with a <Biochrom SimpliNano spectrophotometer> to check that the purification went well:

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/4/47/Biochrom_SimpliNano_spectrophotometer_loading_sample.jpg/262px-Biochrom_SimpliNano_spectrophotometer_loading_sample.jpg]
{height=400}
{titleFromSrc}

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/f/f4/Biochrom_SimpliNano_spectrophotometer_result_readout.jpg/360px-Biochrom_SimpliNano_spectrophotometer_result_readout.jpg]
{titleFromSrc}

And because the readings were good, we put it in our -20 C fridge to preserve it until the second day of the workshop and called it a day:

\Image[https://upload.wikimedia.org/wikipedia/commons/thumb/f/f7/Minus_20_fridge_storing_samples.jpg/183px-Minus_20_fridge_storing_samples.jpg]
{height=400}
{titleFromSrc}


Oxford nanopore river bacteria/post filtration purification

ID: oxford-nanopore-river-bacteria/post-filtration-purification