This video has been a life-changer for me. I think every view of this video resulted in a scientific paper. You deserve credit for each one of them. This is a prime example of how science grow. Thankyou.
I feel like crying from how happy I am for coming across this amazing video. I wish I could subscribe to your channel a million times. Thank you so very much.
I have never commented on a youtube video in my life, but I have to make an exception. This is an amazing explanation and tutorial on finding an unknown gene sequence of a known protein. This helped me so much. Thank you!!
For the very first time someone made these complicated things easy for me.. thank you sooo much for such a detailed video. I really really appreciate your effort n skills. Please also make a video on primer designing for different PCR like Qpcr simple pcr thank you
Wow. This is amazing Video. I have been looking for such videos for years. Uploaded in 2019, I wonder why it didn't show up in my search earlier. This is what I actually needed to see. Thank you so much for this.
Thank you so much for taking the time to do this. Wonderful video. Really quick, around 21:34, when you are pasting the 1500bp promoter region into Word, you pasted an extra "A" I believe before the beginning of the gene. There are two A's and I think there should be just one. When setting the EPD sequence retrieval tool from -1485 to 0, the 0 is the first base of the gene. So it doubles the last base, which is an "A". Awesome video though, really wonderful teaching.
Your videos are a life saver. I am about to join a lab working on CRISPR CAS9 technique. I have done my PhD in Mechanobiology, an area very different from this. Your videos helped me to brush-up my Masters in Biotech knowledge. Thank you for the videos 🙏🏻
Thank-you so much, bless you, i read these few comments and i swear i feel the same your video made it soooo easy for me to understand it just in a few minutes, it took me months to find solution to my problem and use these software's once again thanks a lot sir
These videos are extremely useful for me as a Biology student. I have recently binge watched all of your educational videos especially the Primer design, gene cloning videos. So thank you so much. Please do not stop making these videos. Would love to learn more about laboratory techniques, molecular and cell biology from your channel.
1500 bases is the average size of a promoter. Some are definitely smaller and some are definitely larger while others cover tens of thousands of bases when you include topologically associated domains. So in short, 1500 is really just a "best guess" to start, then you would have to truncate the promoter from there to determine the actual size of the promoter.
Hi Jacob and thank you for this helpful video! Regarding PROMO- I was wondering if there have been any changes or issues affecting its availability since I have been unable to access the website recently...
Thank you very much! I would appreciate if you might add a comment on how to proceed if for my gene of interest I see - strand in the EPD? Should I invert the sequence to get the correct promoter?
Hi, I found when we set "0 to TSS" in EPD, the last latter was the 0 position of the TSS, which is the first letter of TSS, here in your video was "A", so I think when we copy it, it should be deleted. :)
19:22 Why you select 15 bp before ATG in '' mRNA '' sequence to get promoter region? After I tried this, the result sequence didn't fit with mRNA sequence from ncbi. After that, I realized that there are introns between TSS and ATG in my chosen gene's genome sequence. Promoter region is before TSS, and introns also are transcripted which will be cut off during transcription. So, I think if we should select -1500 to 0 bp relative to TSS in EPD website?
Hi, first of all its a very helpful video. Could you please explain why did you consider only 1500 bp while adding the sequence range in Eukaryotic Promoter Database?
After obtaining the designed gRNA from CHOPCHOP, why is it necessary to have upstream and downstream primers? Can't we directly synthesize the gRNA and then add an oligo? What is the purpose of designing upstream and downstream primers?
You are amazing Sir! Thank you so so so much!!! I am a PhD student in Molecular Biology and I found that video terrific! Can I do a donation to support your work?
Hi Jacob ' you did a brilliant presentation ' however i'm a beginner and still confused.Although it's not my field specifically but i need to choose a short dsRNA sequence of 20 or 27' 28 nucleotide sequence for application in plant but i am not familiar the specificity of the sequence if we had a genome like choloroplast genome and split that sequence into primers can we choose the shortest sequence ? Wether it will work or not??
the coding sequence for my gene starts at 1bp to the end. so my entire gene is a coding sequence... im stumped trying to find the UTR 5' AND 3' please help
Thank you so much for this well explained vedio. I would like to see tutorials related to how to find similar motif to some known steoird receptor binding sites for example PGR, ESR, AR etc.
Hey Jacob , thank you for such a great video ! I was wondering when designing guide rna from the mRNA transcript do we use the exact sequence or one which is complementary ? additionally is there a need to use U instead of the T as I have seen some strands using this base . Thank you
Hi. Do you have any information on the database for Transcription factors for Filamentous fungi such as Trichoderma, and Aspergillus as PROMO doesn't contain these species?
I would like to extract the promoter sequences for 50,000 genes. I have both the Gene GFF file and the genome file available. Among 50,000 genes, 25000 genes are - strand. Could you suggest some other tools?
Everyone who learned from this video should always be awared, especially those who are designing experiments related to DNA, genome or chromatin... NOT ALL the transcription start sites are in the first exon of the gene and also MOST of the genes contain intron in DNA level...
Dear Jacob Elmer, could you, please, tell if gRNA can "cut off" some part of the mRNA? I mean if a gRNA cuts at i.e. 15nt after ATG can it lead not just to the frame shift, but also that these 15 nt would be cut off? And the corresponding domain of the protein would be knocked out?
This video has been a life-changer for me. I think every view of this video resulted in a scientific paper. You deserve credit for each one of them. This is a prime example of how science grow. Thankyou.
I feel like crying from how happy I am for coming across this amazing video. I wish I could subscribe to your channel a million times.
Thank you so very much.
mutual feelings!
I totally agree
Couldn’t agree more.
You do not even know how helpful is that for me right now!!!! Very grateful for this tutorial! :) Create such videos more often
I have never commented on a youtube video in my life, but I have to make an exception. This is an amazing explanation and tutorial on finding an unknown gene sequence of a known protein. This helped me so much. Thank you!!
For the very first time someone made these complicated things easy for me.. thank you sooo much for such a detailed video. I really really appreciate your effort n skills. Please also make a video on primer designing for different PCR like Qpcr simple pcr thank you
So true! I feel the same.
The best tutorial in the history of tutorials!
Wow. This is amazing Video. I have been looking for such videos for years. Uploaded in 2019, I wonder why it didn't show up in my search earlier. This is what I actually needed to see.
Thank you so much for this.
The best explanation I have came across so far
I want to give you a hug, thank you so much. You are helping people.
Thank you so much for taking the time to do this. Wonderful video. Really quick, around 21:34, when you are pasting the 1500bp promoter region into Word, you pasted an extra "A" I believe before the beginning of the gene. There are two A's and I think there should be just one. When setting the EPD sequence retrieval tool from -1485 to 0, the 0 is the first base of the gene. So it doubles the last base, which is an "A". Awesome video though, really wonderful teaching.
Your videos are life saving! Thank you
Your videos are a life saver. I am about to join a lab working on CRISPR CAS9 technique. I have done my PhD in Mechanobiology, an area very different from this. Your videos helped me to brush-up my Masters in Biotech knowledge. Thank you for the videos 🙏🏻
Thank-you so much, bless you, i read these few comments and i swear i feel the same your video made it soooo easy for me to understand it just in a few minutes, it took me months to find solution to my problem and use these software's once again thanks a lot sir
These videos are extremely useful for me as a Biology student. I have recently binge watched all of your educational videos especially the Primer design, gene cloning videos. So thank you so much. Please do not stop making these videos. Would love to learn more about laboratory techniques, molecular and cell biology from your channel.
Hey Jacob, Just awesome man...Just Awesome such a great video after a long time I watched!!
I cantvthank you enough for teaching it in wonderful way...love from India❤
very helpful video...keep uploading such contents.
Very useful video. Thank you sir. Please keep uploading more informative videos like this.
Amazing lesson. Could you also give a lesson using Konck-in approach?
What was the reason for choosing 1500 bases ? Could you please explain?
1500 bases is the average size of a promoter. Some are definitely smaller and some are definitely larger while others cover tens of thousands of bases when you include topologically associated domains. So in short, 1500 is really just a "best guess" to start, then you would have to truncate the promoter from there to determine the actual size of the promoter.
@@jakelmer1985 Thank you. And yes.... I also have seen people choosing more than 2000 .
It's a great tutorial.
@@jakelmer1985 the 5'UTR sequence before the start codon , is that also called as promoter?
Puja thacker no 5’UTR is not the part of promoter
@@pujathacker3879 No, it's the part of gene.
Very much informative but easily explained video! thank you very much
Thank you very much for such useful & helpful video! You save me!
Hi Jacob and thank you for this helpful video!
Regarding PROMO- I was wondering if there have been any changes or issues affecting its availability since I have been unable to access the website recently...
Very helpful and clear! Thank you so much
wonderful explanations Jacob. Please make more
Thank you very much! I would appreciate if you might add a comment on how to proceed if for my gene of interest I see - strand in the EPD? Should I invert the sequence to get the correct promoter?
how did you decide 1500bp upstream of TSS?
Hey Jacob Elmer, I don't quite clear in exon junctions as you explained.
If the gene is on the reverse strand, should I then convert the sequence to its reverse complement in Entrez before doing any further analyses?
Hi Jacob, great video, thanks!
Very usuful and exhaustive for me. Thank you
Hi, I found when we set "0 to TSS" in EPD, the last latter was the 0 position of the TSS, which is the first letter of TSS, here in your video was "A", so I think when we copy it, it should be deleted. :)
Many thanks for such a well-explained video.
thank you for such a great presentation
19:22 Why you select 15 bp before ATG in '' mRNA '' sequence to get promoter region? After I tried this, the result sequence didn't fit with mRNA sequence from ncbi. After that, I realized that there are introns between TSS and ATG in my chosen gene's genome sequence. Promoter region is before TSS, and introns also are transcripted which will be cut off during transcription. So, I think if we should select -1500 to 0 bp relative to TSS in EPD website?
Thank you so much , this was amazing , well explained and in all details
Thank you for the video! Extremely helpful
IT IS EXTREMELY HELPFUL.
Such a great video! It helps a lot. Thanks very much.
this video helped me a lot. Thank you Sir!.
How can we select antisense strand in EPD?
Your videos are awesome! Thank you.
I m working on bacteria, and it's working on this to find the promoter in the bacteria?
How do we know the 618th position we can't just keep reading the entire sequence length?
Hi, first of all its a very helpful video. Could you please explain why did you consider only 1500 bp while adding the sequence range in Eukaryotic Promoter Database?
How can I get the transcription start site of ruminats?
Many thanks for this. Really helpful
Thank you so much. That is really helpful!
A great video Jacob. Keep publishing more.
Subscribed with thanks :)
Very helpful Video. Thank you
After obtaining the designed gRNA from CHOPCHOP, why is it necessary to have upstream and downstream primers? Can't we directly synthesize the gRNA and then add an oligo? What is the purpose of designing upstream and downstream primers?
You are amazing Sir! Thank you so so so much!!! I am a PhD student in Molecular Biology and I found that video terrific! Can I do a donation to support your work?
Great video. Much help!!!
I have a question. Can a mutation in an intron part of a gene convert the intron into an exon?
thank you so much for your wonderful video, it really helps!!!
Amazing, really helpful
How to find AT or GC rich region in a sequence?
Hi Jacob ' you did a brilliant presentation ' however i'm a beginner and still confused.Although it's not my field specifically but i need to choose a short dsRNA sequence of 20 or 27' 28 nucleotide sequence for application in plant but i am not familiar the specificity of the sequence if we had a genome like choloroplast genome and split that sequence into primers can we choose the shortest sequence ? Wether it will work or not??
3:20 Promoter active , recruiting r n a polimerates to transcribe genes, encourages binding
Such a great lecture!
How to solve the problem in case that EPD give you three promoters for one gene, which one is preferred for study of TF.
the coding sequence for my gene starts at 1bp to the end.
so my entire gene is a coding sequence...
im stumped trying to find the UTR 5' AND 3'
please help
What do I do when I have to analyze a gene on the reverse strand??
Did you get the answer?
Thank you so much for this well explained vedio. I would like to see tutorials related to how to find similar motif to some known steoird receptor binding sites for example PGR, ESR, AR etc.
Much help! Thanks a lot!
Thank you sir! Sir i want to check my primers is reverse or forward. For that i want to know the gene sequnce. Can you u please suggest me?
what about the Xenopus tropicalis? please inform me.
thanks a lot, very useful.
pls do more vids about genome brousers platforms.
9:30 the entire transcript sequence.
Please also upload the links you used in your lecture so that we can follow them properly. Thanks for the vedio
cool video! so useful it is！
Thank you very much.
Thank you so much
why -1500bp for promoter sequence?
My sequence from EPD (the capital after the promoter region at 16:42) does not match with the mRNA that I found on NCBI.... What can I do?
Hey Jacob , thank you for such a great video ! I was wondering when designing guide rna from the mRNA transcript do we use the exact sequence or one which is complementary ? additionally is there a need to use U instead of the T as I have seen some strands using this base . Thank you
Hi. Do you have any information on the database for Transcription factors for Filamentous fungi such as Trichoderma, and Aspergillus as PROMO doesn't contain these species?
Thanks...very useful
Hi Jacob why there is no signal peptide in the NCBI and no annotation available in UNIPROT too. In that case can I select the Exon 2 as a target?
Thank you so much !
you saved my life. i wish i could make u some cookies. thanks a lot for this amazing video.
How to get promoter of cow genes instead of human
I would like to extract the promoter sequences for 50,000 genes. I have both the Gene GFF file and the genome file available. Among 50,000 genes, 25000 genes are - strand.
Could you suggest some other tools?
Please make more videos on base editing andcprime editing ❤❤❤plzzz
thanks so much i really need it
Correlate with UCSC genome browser promoter retrieval
Thanks
Everyone who learned from this video should always be awared, especially those who are designing experiments related to DNA, genome or chromatin...
NOT ALL the transcription start sites are in the first exon of the gene and also MOST of the genes contain intron in DNA level...
Dear Jacob Elmer, could you, please, tell if gRNA can "cut off" some part of the mRNA? I mean if a gRNA cuts at i.e. 15nt after ATG can it lead not just to the frame shift, but also that these 15 nt would be cut off? And the corresponding domain of the protein would be knocked out?
Cas9 cannot react with mRNA, but there are other types (III and IV) of Cas enzymes that can cut RNA.
www.ncbi.nlm.nih.gov/pmc/articles/PMC6013697/
Can you please talk for hours on Chipseq Data? Believe me I am ready to listen to every detail. 😊
and thank you so much for this
Hi
Can you please help me cross check my gRna