Video

notes - Zymo Research HostZero Microbial DNA Kit (used for shotgun sequencing) - 16S error correction tools: > Divisive Amplicon Denoising Algorithm 2 or DADA2, an open-source R package that improves on the DADA algorithm > Quantitative Insights Into Microbial Ecology or QIIME (canonically pronounced 'Chime') - 16s bioinformatic tool: PICRUSt (pronounced “pie crust”) or Phylogenetic Investigation of Communities by Reconstruction of Unobserved States, written in Python and R Thanks for this wonderful video. 🌞

How do i store the filtered dna?

this was an excellent video, thank you so much! The autocorrect made me laugh, as this has victimized me in the past.

Thank you so much it was really helpful

For how long should you thaw on ice?

Thanks for your presentation, what is the tool to find DMR in your research?

Great🎉and thanks

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Looking forward to see the results

fantastic video, thanksss

If I want to measure Methylation of protocadherin 17 human gene in gastric cancer cells before and after adding of dnmt1 inhibitor what is methods can be used ?

Can it be stored for a prolonged period of 6months

Hello Zymo, Can i use a thermo mixer in place of Bead beater?

Tip to increase plasmid yield exponentially: Before using kit, spin down 1mL of culture and discard supernatant. Re-suspend in 1:1 LB and H20, ~600uL. Continue using plasmic miniprep kit as instructed. This technique has increased yield 7x in some cases. Hope this helps someone else!

Increase NAD, decrease CD38 and control body inflammation seems to be the way right now to live a long healthy life that the average person can do right now.

how do we know if the sequence is or isn’t conserved?

thank you this is amazing

Hi, can I use a power lyzer instead of the bead beater? and for how long? Thanks !

Great video, thanks so much

Can you also explain to me a bit what do you mean by cross-domain coverage?

Hey Zymo Research... pls do you have in store some references discussing about metagenomics vs metabarcoding to share with us (me especially)? Thanks by advance!

At the initial TRizol/Ethanol mixing step, would using 100% Ethanol instead of 95% Ethanol affect the RNA yield from the extraction

This kit can be used for gram positive bacteria plasmid Dna isolation?

This was a great presentation. Thank you!

I think the instructor should slow down as speedy talk make understanding such technical topics more difficult.

BS sales spiel. Tested negative with rapid and PCR, two days later at an airport tested positive. Came back to retest with a negative. How about a statistical report on how testing sites are following protocols…

Thank you very much for this detailed and excellent presentation. Btw, I used Zymo RNA Concentrator during my extraction :)

Why does the speaker need to speak so fast when explaining a technical topic?

Thank you for the helpful information! Really appreciate it

How large of a pellet is too large?

I believe I've created an epigenetic emotional and mental psychological tool that's getting 100% results in resolving the cyclic negative behavioural patterns. I built it based on realising you have to work within a bloodline to be sure you get the root. Although I've got hundreds of real people case studies, I don't have anything scientific. I think this is a mahout missing live of the puzzle and it's organic. I also don't have the funding for an official study. Although my tool is now used in 20 countries by therapists. It really is a one of a kind. I think all studies need to also be segmented into males and females. Keep up the great work guys.

This is a really nice video. Very helpful!

Great video. I have a question. In the first scenario it was around a 9% chance of a false positive and an almost 0% chance of a false negative. Do labs do any additional calculations to combine the two (positives and negative numbers) to give a more accurate result? Basically I’m trying to work out in the first scenario if the person got a positive result then does that mean it’s 91% accurate or is it more accurate than that when you factor in the negative numbers?? Hope that makes sense…

Hi, Could you please tell me how deduplication of the alignment was done using Bismark ?

Is the strong smell during the preparation harmful to us?

How to index reference genome using bismark....please share the command usage

Is this feasible for RNA purification?

Would the blood transfusion of which you spoke have a positive outcome for infertility cases?

Really helpful sir. Thanks a lot.

Is it that hard to put subtitle really?

Great video! A suggestion for something you could do in the future might be to make a video comparing Amplicon Sequencing and Shotgun Sequencing, as 16S is just an example of an amplicon. You state that the use of 16S region limits your study to just bacteria, but other highly conserved regions can be used to target members of the other domains, like the 18S and ITS regions like you mentioned at the end.

If i were to use ASV, do I still need to run DADA2 or amplicon denoise before hand?

Why are there no error correction tools for shotgun sequencing?

Thanks for the video Doc :) A good explanation. I have a question though. From what I understand, at the current moment... we cannot know whether someone has covid-19 without doing the RT-PCR test, right? ... One can only know whether they are infected only based on this test. The thing is... when people talk about FP and FN (false positives and negatives) ... one thing that is required is the actual number of positive (true positive) people and also the actual number of those without the disease (true negative).... Now... since we don't have any true positive numbers (since the RT-PCR itself is not a gold standard)... how can FP or any other metric (e.g. sensitivity, specificity, or even FN) be reported or calculated? Ideally (or supposedly), before the RT-PCR would even be administered... one would have to have a sure way of knowing whether a person has the disease or not. Say this is done through isolating and purifying test subjects samples and absolutely determining whether or not he/she has the virus. In short, this is the gold standard... where the ground truth is known (meaning we know who actually has the virus, and who does not have the virus). Then, after these subjects have been properly classified.... then we run the RT-PCR on them... to see which patients are classified as +ve and which as -ve. .... and only then can we calculate the false positive (or whatever other) metric, right? Now... with the absenece of such subjects... how can we say that the RT-PCR has a FP of such and such? Or an FN of such and such....? Please note that this is not a negative comment. I am just trying to clarify based on what I've learned in my research on how to calculate false positives, sensitivity etc. :) Thank you!

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Could you introduce how to analyze differential methylation when you are free? And the theoroy about how to get methylation signal as well as interpret it in detail .

This doesn't explain the tests ability to recognize any coronavirus antibodies that have resulted from The Common Cold. You need to add that into your data to increase the odds of a false positive including a biological aspect. See CDC website regarding.

Curious how cheap I could drive sequencing for some very low complexity population samples. I'm interested in getting full genomes for some samples that probably have 10 or less species/strains as cheap as possible.

This is fantastic thank you folks so much!

Thanks for uploading ~ Great video, it provides an informative insight into the two methods.