Gene Expression Analysis and DNA Microarray Assays

If we want to understand a biological organism, we turn to the expression of its genome. Which genes are being expressed, and in which cells, and when? How does this differ between a normal cell and a cancer cell? We have incredibly sophisticated techniques to investigate these questions, and the most indispensable is the DNA microarray assay. This apparatus is even more useful than it is colorful, so let's see how this works now.
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[@jamilakalilj]

Currently, using this to supplement my Master's program. The visuals helped to solidify my readings. Thanks, Dave!

[@mariemasarikova8575]

This is a quite old comment I know, but wanted to let you know that it's comforting to see that even a master's student needs clarification on this. I'm doing my bachelor's and currently battling imposter syndrome, so thank you.

[@m.b.k642]

@@mariemasarikova8575 I’m doing this as a 16 year old , SED

[@aahana8816]

@@mariemasarikova8575 same, seeing so many comments from masters students is making me feel better about not being able to grasp the concepts of such techniques easily

[@lashazhvania6813]

@@mariemasarikova8575 Haha, thanks for clarifing my syndrome= imposter syndrome-" It disproportionately affects high-achieving people, who find it difficult to accept their accomplishments" I thought i was able to find cure for HIV :D

[@robinletourneau3567]

I just wanted to give a heartfelt thank you for this video. My first year final tomorrow is an essay about using microarrays to identify heterochromality genes in huskys and this helped me study for it tremendously.

[@giov6538]

This is great: super simple, super precise, it makes you really understand the basis of microarrays. From here you can go to more complex videos, but you do need a basis like this to start! Congratulations

[@riecchi]

thank you SO much. i was struggling to understand amidst so much stress but this completely cleared up my confusion and i could not be more grateful right now

[@narayanappam6482]

Professor your explanation is informative, precise and beautiful thank you

[@bracken7794]

Many thanks for this explanation professor Dave!

[@camilaglee23]

Thank you very much, you helped me understand much better. Greetings from Argentina!

[@thestudymuse_myrsini]

Thank you so much for the effort you put into this, its was so easy to understand

[@victoriariosvazquez2924]

Watching this to clarify my mind on my thesis proposal tomorrow, you're a life saver! THX

[@user-le6hp6vr7b]

The explanation was excellent !! i used it to explain the DNA chips for my students

[@ratethingies6139]

Huge thanks jumping from Saudi to you and the channel!

[@hfof]

omg. You are so talented man, the more I grow up, the more I realize how genius and knowledgeable you are. Cheers to you from Saudi Arabia.

[@sainidhi5617]

Amazing video👌👌👌. It was really helpful. Now the concept is clear for me. Thank you soo much for this video 😃.

[@asmashakir7859]

Thanku very much professor your video really helped me in understanding microarray the way u explains is best

[@semb12]

I'm doing a biochemistry masters and this is helping me - thanks.

[@atxbee]

thank you for everything you do!! :)

[@krishnaprasad5508]

thank you for your content. you explained it beautifully

[@KnighteMinistriez]

I really like how you explain the science. I like these video.

[@swarnavadutta4648]

you just nailed it🔥 love from India💝

[@songthanh896]

Really helpful, Professor!

[@mongotrip9999]

good work! thanks from austria!

[@natasharasebotsa7300]

i struggled with this for a long time. Thanks a lot

[@ThaoLe-kw2ij]

Super helpful! Thank you very much!

[@i.am_pluto4012]

Thank you prof Dave... Much love!!!

[@PoojaSingh-kk6qp]

Thank you sir very beautifully you explain the procedure

[@Omxralb]

I FREAKING LOVE YOU PROFESSOR DAVE EXPLAINS!!!!!

[@lilsnaps6881]

you sir have just saved my grade, i salute you o7

[@jorgrudiger2894]

Thanks. I watched it just for general interest in this subject.

[@lewietlewiet2632]

Why getting a 90€ Biochemistry-Textbook when KZbin can help you to understand the topic in about 8min? :) Thank you for your content! It helped me a lot! :)

[@oldmedstudent1750]

Dude seriously. I'm learning Biochemistry and required to use the Lehninger book that everyone says is so good but I honestly am learning so much more from KZbin and only refer to the book when I have to. I'm getting along just fine without it.

[@mohamedabdelhamid5771]

Thank you very much , Professor ❤❤❤❤❤❤🙏🙏🙏

[@annielyncy281]

Wonderful presentation and thankyou 👌

[@marhabourinboyeva9025]

Thank you so much. This video is really helpful 😃👍

[@ummehabiba7612]

great work! so much helpful in my Master's

[@roohisakina5742]

Very impressive explanation.

[@emannadeem3168]

Thank you Professor Dave 😃

[@mustajabalam3794]

Plz make video on validation and QC of flowcytometry and molecular techniques like RFLP ,SSP and SSOP

[@arezoojokar-pn5si]

Amazing video. Thank you ❤❤

[@Tigerbear1068]

Thank you ! This helped me so much !!

[@JasonCarlson]

Totally dig your style and material! Go Science and kick some assays..

[@Ravezmalazada]

Thanks, I hope you make video about RNA microarrays, it will be so completable !

[@hamidkiangaikani]

Awesome! Thank you.

[@carlosmonf]

Thanks for the info you made it see easy

[@amirsh9710]

that was so helpful thanks prof😉

[@alizaalam7624]

thankyouu😌 I never understood microarrays in my class

[@user-fn2xc7dz1i]

Thanks Professor Dave

[@ismaelnaruto30]

Wow, nice video man

[@alicelidman6327]

Thank you so much for the video! I have a question. Does the cDNA have to be denatured, like with NaOH or something, so that it can bind to the single-stranded probes in the array?

[@Echodonut]

yes.

[@wassmmd8521]

Good work

[@user-rk2fm3bn3u]

Thank you professor ❤

[@DivineBre]

Extremely helpful

[@adamastiti8606]

Thank you prof

[@drshreyaagrawal7285]

Amazing !

[@ma.8805]

YOU ARE THE BEST

[@leonr.8084]

Thanks so much, helped a lot for my coming exame!! Greetings from Germany

[@Dinamite4]

What kind of sequencing can you perform that Dave explains at 7:15? can you do Next gen sequencing?

[@nnankegracearikpo2847]

Very helpful ❤

[@nolifeols]

Could you please make a video explaining RNA sequencing. Thanks.

[@ssvr]

Is this this DNA microarray process described in the video also known as "bulk" RNA sequencing?

[@aimenmustafa62]

Every time Authentic content ...

[@larysavynohradova8845]

отличное видео, наконец все стало понятно))

[@sushmanepal1240]

Thank you so much !

[@mass_oak]

great content

[@kajalgaur3362]

One of best😍

[@sujis142]

Thankyou sir ✨

[@tolerafufa5683]

VERY NICE

[@huihuihuihuihuihui1]

Nice!

[@rzellereyes1932]

So for microarray, we are only using one cDNA strand which was made from the template, the mRNA. However, there is one thing that isn't clear to me and that is about the RT-PCR. RT-PCR generates double-stranded cDNA right? How come in microarray we are only using the single strand and not double? Is there any intermediate enzyme that was involved?

[@Simi.g]

thank you

[@moonyqasem6186]

Thank you so much ❤ your my hero 🦸‍♂️

[@smitshah8074]

thank you sir

[@detectedoutside8155]

How have you not already made a connect four?

[@jananishambhasivam7952]

Tku sir I wish I could have been your student.

[@elfa4231]

Does this mean that we need to have a full genome sequenced of that specific organism in order to construct the microarray plate?

[@sciencenerd7639]

amazing

[@meryemlahbara2834]

❤❤ thank you

[@maylia3132]

this man is a legend i have an assignment due tmrow that if i fail im gonna have a 70 and this man just saved me

[@jonathankimkful]

med student here. wish our professors can teach like this...

[@ananyayadav9686]

This was so amazing...but not gonna lie , the lizard freaked me out a little bit.

[@saroshvachha1588]

100000 times better than my textbook

[@thadbonzon]

Could someone explain, how do we know where the complementary strands in the microarray came from (as in, from cell type 1 or cell type 2)?

[@sofianbio4997]

Thank you please more things explain about genotype

[@magosInformaticus]

I'm a little confused that the approach is to make double-stranded DNA with DNA polymerase and then try and get it to apparently separate and bind to single-stranded probes. Do the probes test for both the sense and antisense strands on each spot?

[@samoleulmi990]

Same issue here , couldn't manged to understand that point.

[@Behillod]

Hey, you might already have found the answer to your question but in order to make cDNA we use a reverse transcriptase. This is a protein that basically turns your RNA back into DNA. Usually the reverse transcriptase leaves you with a single stranded DNA strand and a round of normal PCR (polymerase chain reaction) is required to turn it into double stranded DNA. Hybridization can then be performed by separating the strands again (either heating or chemical, where heating would be preferred since it is less harmful for the DNA). The stand that is complementary to the probe that was designed will then bind to either one of the strands and start the microarray assay. Which strand binds should not matter too much since the probe should be specific for a certain gene. Hope this helps.

[@rowanessam9154]

you are a legend

[@shahryarkhorasani137]

Thank you! One Question: How the RNA splicing during post-transcriptional modification does not cause any problems for RT-PCR?

[@IntellicastFacts]

In a nutshell, RNA splicing involves the removal of introns (non-coding parts of the mRNA) and joins the coding sequences (exons) together in order to enable translation. Since the parts removed are non-coding, it does not affect RT-PCR. RT-PCR, standing for Reverse Transcription Polymerase Chain Reaction, involves reverse transcriptase - converting RNA into cDNA - and (often) Taq DNA polymerase - completing the DNA after denaturation. To sum up, since the RT-PCR process only duplicates CODING DNA, DNA splicing does not affect the process AT ALL, since it removes NON-CODING parts of the original DNA.

[@jaykay8098]

word of caution, rna pol doesnt need a primer right, so reverse transcriptase having a primer feels fishy but its not because although widely called reverse trasncriptase the enzyme itself is synthesizing dna and so in essence its a dna pol and dna pols need the TTT primers.

[@tolerafufa5683]

YOUR LESSON IS ATTRACTIVE AND GUIDELINE FOR US. BUT I HAVE A COMMENT. HOW CAN I CONTACT YOU PERSONALLY?

[@azifahahmed4462]

I have a question How could you use Gene Expression Arrays to identify alternative splicing

[@calebm9000]

Some researchers have used algorithms to study expression differences between samples. pubmed.ncbi.nlm.nih.gov/11435406/

[@CryptoBountyHunt]

My question is mRNA already bound and complementary cDNA is formed then how they bind with dna probes present in wells

[@berndelignie8002]

Wont you use q pcr for expression?

[@mustajabalam3794]

Great

[@vasundhararaina6849]

so you mean a common pool with all the different samples is allowed to hybridise on the array

[@TheMrCazano]

Microarrays are rarely used anymore. RNA-seq and even single cell RNA-seq (scRNA-seq) is much more common now.

[@clashwithsparkcrazygamers]

During the process of RT-PCR we get a complimentary ssDNA for which we perform PCR to get a dsDNA, we add this to each of the wells of the array plate and the complimentary DNA probe hybridizes and form a link. My doubt is if the DNA is already ds post RT-PCR how will it bind to another DNA probe. Or are we considering the DNA to be ss post RT- PCR. (the animation does not support the fact that the DNA is ss post RT-PCR at 5:11 ) Anybody?

[@polymath5093]

I have a question here.. Do we amplify cDNA before introducing it to the Array? If yes, we already used a primer to amplify our gene of interest.. In this case, how different genes in the array well would produce color except the one we amplified with our primer? If we don't amplify, how the trace amount of different cDNAs will produce color in array?

[@prabhar4254]

Actually..i had the same doubt b4...but now i got to know that if we are adding gene specific primer means, no need to go with microarray since it is a highly powerful tool for differentially expressed genes not for gene expression, i think...im not sure about it.....if you know something means, please leme know bcx iam having a seminar on bee nutrugenin ICS..

[@adnanqamar7815]

Genius

[@julianasuarez7974]

How is the double stranded cDNA "split" into a single strand to hybridize with the probes in the microarray?

[@nurajafar8366]

An RNAse endonuclease would have to disassemble the RNA molecule from the cDNA, to allow for the hybridisation

[@cdorman11]

Heating, same as for PCR with DNA polymerase

[@caddyshackwizard9367]

Is it me or does it seem like Dave's videos are being suppressed the amount of views to subscribers just does not add up

[@ProfessorDaveExplains]

Nah it's just that people subscribe for so many different subjects, any given video will only appeal to a small percentage of them. But spread the word!

[@fidamuhammadkum]

please sir discribed the discovery of drug through micoarray

[@srt4721]

Hats off ^_^

[@sebastianjabine8791]

thank you science jesus