Finally somebody explaining how the technique actually works. Over videos are so vague and assume you already understand the function of all the parts. Thanks so much
This is the best explanation on NGS. I had no clue, done so many researches but cant understand clearly. But this explanation is just awesome. Thank you so much.
From now on you can become a member of this channel! You will have access to some cool emojis like or . This is of course voluntary, but the financial support helps me a lot.
I have heard some conflicting ideas on what Hybridisation is. One thing I read seemed to imply it was the process of binding the oligonucleotide adaptors to the cut up DNA, however is that not just library formation. Then other places and your video have implied it is when the oligonucleotide adaptors bind to the complementary oligonucleotides on the flow cell.
I have a question, so at the end of the vid is DNA read of only 1 small cut fragment, how do we combine all fragments that have been cut at 0:31 1 little fragment is analyzed by overlaid fragments result from PCR, then what about the whole thing, I mean restriction enzyme will cut it nicely and no overlaid could happen
Remarkably explained! Tho I have a question. If we want to seq the foreign DNA in one go...why do we discard the Reverse based strands, cos if we would keep them, the sequencing will only mark out the initial forward strand and that's what we are aiming for! Still confused.
Very good explanation, but I have one little question: How can it be that the two different Adaptors bind to the two different ends, and not one adaptor to both ends? Is the cutting done by a restriction Enzyme, and therefor it always has the same Nucleotides at the end?
1. It's cos one is Forward primer and the other is reverse primer that's why they join different ends. 2. Yes the restriction is done by a single restriction enzyme, so that the sticky ends are poduced uniformly, and yes the overlapping sequences indicate that they are cut by Restriction endonuclease that's why they overlapp and give us full strand of interest. Remember! We didn't know what the DNA seq was to begin with, it can be some sort of Virus or other microbe but we don't know which!
Paired ends. When doing an alignment one is chemically specified to left side and one to the right. It labels the 5' and 3' ends appropriately for alignment sequencing with something like SPAdes.
Hi! This video is great but I still struggle to understand the process. At 01:29, we have a single-stranded forward fragment which is hybridized to the blue oligos and then PCR occurs and the fragment is amplified. In this step, is not happening the same with the reverse fragments, which are hybridized to the red oligos and amplified? What changes in the second step with the bridge building, why is it necessary? I'd really appreciate if someone can help me understand! 🙂
Thanks a lot for this incredible explanation. Anw, I have some questions : 1. What is the purpose of DNA fragmentation? Is there any specific site for this cutting? 2. Regarding the adaptor, would you mind to explain more about the constituent of this? Is it like primer where we should design it first? How the adaptor can recognize the end of the fragmented DNA?
The DNA is fragmented to enhance the speed of the sequencing (it's faster to sequence a lot of tiny bits, than a really long chain), and to reduce the "mistake" rate of the polymerase. plus, the polymerase can fall off if the sequence is extremely long
It is great indeed. One question, why do we need to pcr amplify a single strand into many copies in a same spot? At the end isn't it just sequencing a single strand on a particular spot?
@@henrikslab during sequencing reaction after each nucleotide is incorporated, the terminator is removed, as well the fluorescence molecule. Why 1000 to 5000 copies of a single strand is required in the same spot or cluster?
I have 1 confusion! A single strand has adapter A on one side and adapter B on the other side or end! When it is added to flow cell and its adapter A side binds to its complementary oligonucleotide and DNA generates a complete strand, then the orginal strand is denatured and wash away. Now the strand which is left stand! How can it form a bridge when it is not carrying the sequence of adapter B but its complementary sequence?
What is NGS sequencing? For that what we do first is fragment our DNA. Each fragment will then be attached to two adapters, a side chain nucleotide binding sequence and an oligonucleotide that will bind to the flow cell. The DNA is denatured and the fragments then attach to the flow cell. Here DNA amplification by PCR results. The unattached atrand is washed away. Hence, bridge amplification is carried out where the strand attached via both it's ends to the flow cell and the PCR is carried out. In this way, both the strands are attached to the flow cell. After several rounds we have the amplified DNA. Having both forward and reverse strands. The reverse strands are washed away and the forward strands undergo sequencing by synthesis Here each strand has primer attached and one by one a fluorescently labeled nucleotide attaches to the DNA, which is detected each time a nucleotide is incorporated, once the DNA fragments are replicated and nucleotide for one particular strand is detected along with for other strands, bioinformatics tools are used to determine the sequence of entire fragments by placing the sequences side by side and determining the sequence overlaps. The sequence are compared to reference genome
I have a doubt. Bridge building occurs with both forward (5' to 3') and reverse sequences (3' to 5') right? So when, a bridge is formed by reverse sequence, the amplification of forward sequence is continuous and when a bridge is formed by forward sequence (5' to 3'), the amplification of the reverse sequence is discontinuous (3' to 5') as we see in traditional DNA replication by the formation of Okazaki fragments?
Don't know the exact case scenario... but in case you sequence cells of an animal such as "Fish X", you may use the reference genome from the most closely related animal of which the sequence is known/published!
There are multiple ways to do so. But in many cases the "tweezers" scientists use are enzymes, that bind to specific or in other cases more unspecific DNA and can delete (cut out) base pairs or even add (insert) new ones. A cool example of how to manipulate DNA is the CRISPR Cas9 system... See here: ua-cam.com/video/4knIPgD6h1U/v-deo.html
I feel stupid cuz everyone's like.. this is the best explanation I've ever found! And I *still* don't know what the hell he's talking about im gonna fail rofl
So in order to 'see' the DNA, you need to see the fluorescence, so you need the leading strand to be fluorescent, therefore needing copies of the template strand.
Does the fluorescence of the paired nucleotides goes away when it pairs to the DNA? I mean, if the sequence comes to be yellow-blue-yellow-blue as in TATA boxes for example, would it emit green light because of the combination of the colors?
Hey, I´d like to use some screenshots of your graphical illustration in a powerpoint presentation, if that´s okay for you (master student seminar, im a student)? - really liked your video, it made understanding Illumina much easier! Thank you so much
Just a request there Henrik. It'd be lovely if there'd be fewer rare, field specific, Latin/Greek/French words in these kinds of videos. Makes it really hard to understand for a layman. So I would really love if you could try and translate these into common Germanic words that everyone knows. Examples: Ligation, DNA Adaptors, sequence, complimentary, hybridize, denaturation, polymirazed chain reaction, synthesized, olegol? nucleotides (genuinely don't know what you said there). I could go on and on. I hope you get the gist of what I'm saying. Would really help a lot of people understand what's going on much more easily.
Thank you for that kind of nice feedback! Yes, I definitely agree with you - I guess the videos are not really designed for a pure layman... most people watching the videos are biology students themselves (so I honestly kind of expect them to know) Nevertheless, I take this point and might think twice before using a specific term. Thanks!
Who else came here cause the illumina video was confusing
😂👋
Me😂😂😂
Meeee
yess 😂
Me😂😂
Finally somebody explaining how the technique actually works. Over videos are so vague and assume you already understand the function of all the parts. Thanks so much
One thing to keep in mind is that adaptors are stuck with the 5’ end to the flow cell so the polymerase can synthesize DNA in 5’ to 3’ direction
Ooooh right thank u
shouldn't it be the other way around? DNA polymerase synthesize from 5', so the adaptor stuck onto the plate should be at the 3' end, shouldn't it?
all the other vids on youtube just kinda goes on a rampage abt how innovative and amazing it is like a promotion or smth. So thank u so much my guy
Incredible well explained. Non of my uni professors have been able to explained that well
That’s what I want to say
Can u pls tell me wt he explained in last I didn't understand that word
same haha... finally got it
💗💗💗💗💐💐🥺🥺
This is the best explanation on NGS. I had no clue, done so many researches but cant understand clearly. But this explanation is just awesome. Thank you so much.
A perfect and clear explanation for the NGS!
Just want to give you a shout- out and thank you for such an easy-to-understand overview of this process. It is definitely helpful.
Thank you!
I wish I found this video earlier lol, spent 2 semesters on this and none of my professors explained it well enough
Now everything make sense to me
yeah, unbelievable how much that matters and how few people are actually competent to teach..
thank you very much sir. This is more well explained than the official Illumina videos.
simple, clear, and comprehensive! Great job!
Excellent, very well explained. Clearing all the concepts one by one
Thank you, your animation and explanation are very clear. I finally understand what happened.
This is truly incredible. Good work.
Mein Professor hat dein Video für die Erklärung genutzt. Sehr stark, weiter so!
Darf ich fragen an welcher Uni, welcher Professor? :D
this is incredibly clear and easy, thank you very much
Great video. The only one that allowed me to understand this difficult topic
This is the best and simple explanation ever in this topic. Great job.
From now on you can become a member of this channel! You will have access to some cool emojis like or .
This is of course voluntary, but the financial support helps me a lot.
I have heard some conflicting ideas on what Hybridisation is. One thing I read seemed to imply it was the process of binding the oligonucleotide adaptors to the cut up DNA, however is that not just library formation. Then other places and your video have implied it is when the oligonucleotide adaptors bind to the complementary oligonucleotides on the flow cell.
I have a question, so at the end of the vid is DNA read of only 1 small cut fragment, how do we combine all fragments that have been cut at 0:31 1 little fragment is analyzed by overlaid fragments result from PCR, then what about the whole thing, I mean restriction enzyme will cut it nicely and no overlaid could happen
God bless you, Henrik!
Great video! Crisp explanation! Much appreciated!
Thank you. Simple and clear. Now I know how it works!
Great explanation - simple and effective!
this should be illuminas explanation video. very well done 👍🏽
Very cool and informative Henrik 👏👍🙏
Besser als mein Prof. es je erklärt hat, Danke für das Video :)
Such a amazing esiyer undesirable way of teaching ❤️ we need teacher like u . Great 👍🙏
clear and easy to understand. Thank you !
sehr gut gemacht hinnerk
Your lectures are wonderful!!!
This is indeed good and helpful, thank you so much
Remarkably explained! Tho I have a question. If we want to seq the foreign DNA in one go...why do we discard the Reverse based strands, cos if we would keep them, the sequencing will only mark out the initial forward strand and that's what we are aiming for! Still confused.
your explanation was perfect but i'm definitely failing my exam tomorrow
If you still read it: All the best for the exam!
Incredibly clear ! Thank you !
thank you so much Henrik. This was perfect!
Thank you so much, you explained it super clearly!
This was an incredible explanation! Thank you so much
Thank you!! This was so helpful, my uni lecture was quite confusing and the illumina video just made it so much worse lol
You save my exam thank you ❤️❤️
Very good explanation, but I have one little question: How can it be that the two different Adaptors bind to the two different ends, and not one adaptor to both ends?
Is the cutting done by a restriction Enzyme, and therefor it always has the same Nucleotides at the end?
1. It's cos one is Forward primer and the other is reverse primer that's why they join different ends.
2. Yes the restriction is done by a single restriction enzyme, so that the sticky ends are poduced uniformly, and yes the overlapping sequences indicate that they are cut by Restriction endonuclease that's why they overlapp and give us full strand of interest. Remember! We didn't know what the DNA seq was to begin with, it can be some sort of Virus or other microbe but we don't know which!
Great video, fast and detailed!
I have a question: Why is a copy done before the Bridge Amplification? Isn't the Bridge Amplification enough for amplifying my DNA?
Thank you for the video. This made my concept much clear now!
perfect explanation, thank you
Amazing explanation and video! Thank you.
thank you for your clear explanation
This is the best explanation✨
Very well defined, To the point. Thank you.
Thank you! This was very helpful :)
Very well explained. Please also explain depth of read and coverage
1:54 what was the point of amplifying the dna fragment if the complementary strand is denatured and then washed away?
Very short and very understandable! Thank you for good work!
Thank you for this vid, but in the compnay video they mentioned an index 1 and idex 2. What are those and which is their purpose????
Paired ends. When doing an alignment one is chemically specified to left side and one to the right. It labels the 5' and 3' ends appropriately for alignment sequencing with something like SPAdes.
very well explained, thank you
Hi! This video is great but I still struggle to understand the process. At 01:29, we have a single-stranded forward fragment which is hybridized to the blue oligos and then PCR occurs and the fragment is amplified. In this step, is not happening the same with the reverse fragments, which are hybridized to the red oligos and amplified? What changes in the second step with the bridge building, why is it necessary? I'd really appreciate if someone can help me understand! 🙂
Yes I was wondering the same thing
Thanks a lot for this incredible explanation. Anw, I have some questions :
1. What is the purpose of DNA fragmentation? Is there any specific site for this cutting?
2. Regarding the adaptor, would you mind to explain more about the constituent of this? Is it like primer where we should design it first? How the adaptor can recognize the end of the fragmented DNA?
The DNA is fragmented to enhance the speed of the sequencing (it's faster to sequence a lot of tiny bits, than a really long chain), and to reduce the "mistake" rate of the polymerase. plus, the polymerase can fall off if the sequence is extremely long
doesnt shorter reads increase the error rate?@@keb_in
It is great indeed. One question, why do we need to pcr amplify a single strand into many copies in a same spot? At the end isn't it just sequencing a single strand on a particular spot?
PCR is required to get enough material for sequencing. Single strands are not sufficient.
@@henrikslab during sequencing reaction after each nucleotide is incorporated, the terminator is removed, as well the fluorescence molecule. Why 1000 to 5000 copies of a single strand is required in the same spot or cluster?
I have 1 confusion!
A single strand has adapter A on one side and adapter B on the other side or end! When it is added to flow cell and its adapter A side binds to its complementary oligonucleotide and DNA generates a complete strand, then the orginal strand is denatured and wash away. Now the strand which is left stand! How can it form a bridge when it is not carrying the sequence of adapter B but its complementary sequence?
I have exactly the same question!
What is NGS sequencing?
For that what we do first is fragment our DNA.
Each fragment will then be attached to two adapters, a side chain nucleotide binding sequence and an oligonucleotide that will bind to the flow cell.
The DNA is denatured and the fragments then attach to the flow cell. Here DNA amplification by PCR results. The unattached atrand is washed away.
Hence, bridge amplification is carried out where the strand attached via both it's ends to the flow cell and the PCR is carried out. In this way, both the strands are attached to the flow cell. After several rounds we have the amplified DNA. Having both forward and reverse strands.
The reverse strands are washed away and the forward strands undergo sequencing by synthesis
Here each strand has primer attached and one by one a fluorescently labeled nucleotide attaches to the DNA, which is detected each time a nucleotide is incorporated, once the DNA fragments are replicated and nucleotide for one particular strand is detected along with for other strands, bioinformatics tools are used to determine the sequence of entire fragments by placing the sequences side by side and determining the sequence overlaps. The sequence are compared to reference genome
I'm liking the Next Generation Sequencing (illumina)
Amazing explanation 🤩🤩🤩 thank you so much!
Superb explanation
really great helpful explanation thank you much
Super clear. Thank you.
I have a doubt. Bridge building occurs with both forward (5' to 3') and reverse sequences (3' to 5') right? So when, a bridge is formed by reverse sequence, the amplification of forward sequence is continuous and when a bridge is formed by forward sequence (5' to 3'), the amplification of the reverse sequence is discontinuous (3' to 5') as we see in traditional DNA replication by the formation of Okazaki fragments?
Very well explained. Thanks!
I’m high school student..
How is DNA synthesized in the 3 to 5 direction in the reverse strand?
Please let me know about reverse strand!!
amazing tutorial, so well explained, made a very complex subject very simple :)
THANK. YOU. SO. MUCH. Really clear
Thumbs up man, it's incredible. Help more.
Thank you so much for sharing. It really helped.
terrific and simple explanation, thanx a lot
Very good explanation. Thank you
If we sequence it for the first time,and we will have no reference genome,then what will do? Plzz must reply me
Don't know the exact case scenario... but in case you sequence cells of an animal such as "Fish X", you may use the reference genome from the most closely related animal of which the sequence is known/published!
How do you manipulate DNA? I suppose you cannot grab them using tweezers, right?
There are multiple ways to do so. But in many cases the "tweezers" scientists use are enzymes, that bind to specific or in other cases more unspecific DNA and can delete (cut out) base pairs or even add (insert) new ones. A cool example of how to manipulate DNA is the CRISPR Cas9 system...
See here: ua-cam.com/video/4knIPgD6h1U/v-deo.html
very clear explanation thank you very much
This is the greatest explanation I have seen about the procedure. Kudos!
I feel stupid cuz everyone's like.. this is the best explanation I've ever found! And I *still* don't know what the hell he's talking about im gonna fail rofl
You're a saviour! Thanks
Thank you so much sir.... You are my savior!
Straight to the point
Use good English with good explanation .
Thanx✌👍👏
Thanks so much, really well done!
Well explained 👏
Great video! very clear thank you
Wanted to ask why do you wash away all of the reverse strands after PCR? Does it matter whether you wash away the reverse or forward strand?
So in order to 'see' the DNA, you need to see the fluorescence, so you need the leading strand to be fluorescent, therefore needing copies of the template strand.
Which topics should I cover in my next videos? Make suggestions below this comment and like the ones you are most interest in
Gene cloning, micro array, protein assay
@@SK-pi6hr Do you mean Western Blot with Protein Assay? Or do you mean some concentration determination of protein (e.g. Bradford Assay)
@@henrikslab concentration determination of protein
@@SK-pi6hr Your wish is granted! Upload: Today :)
I love the explanation
straight to the point
very good. now you can go to my exam and maybe pass
Does the fluorescence of the paired nucleotides goes away when it pairs to the DNA? I mean, if the sequence comes to be yellow-blue-yellow-blue as in TATA boxes for example, would it emit green light because of the combination of the colors?
Adopter is for binding of primer right?? I think there is one more use of adopter. I wanna know about adopter please
You saved me! Thankyou so muchh😭😭❤️
Hey, I´d like to use some screenshots of your graphical illustration in a powerpoint presentation, if that´s okay for you (master student seminar, im a student)? - really liked your video, it made understanding Illumina much easier! Thank you so much
It is ok!
Thank you so much, this was super well explained!
Thank you! Clear explanation.
Just a request there Henrik. It'd be lovely if there'd be fewer rare, field specific, Latin/Greek/French words in these kinds of videos. Makes it really hard to understand for a layman. So I would really love if you could try and translate these into common Germanic words that everyone knows.
Examples: Ligation, DNA Adaptors, sequence, complimentary, hybridize, denaturation, polymirazed chain reaction, synthesized, olegol? nucleotides (genuinely don't know what you said there). I could go on and on. I hope you get the gist of what I'm saying. Would really help a lot of people understand what's going on much more easily.
Thank you for that kind of nice feedback! Yes, I definitely agree with you - I guess the videos are not really designed for a pure layman... most people watching the videos are biology students themselves (so I honestly kind of expect them to know)
Nevertheless, I take this point and might think twice before using a specific term. Thanks!
@@henrikslab Thanks for your response and for considering my advice!
Nice well explained lesson