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.
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
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, 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. :)
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?
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?
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??
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?
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...
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?
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?
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!!
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
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.
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?
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
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?
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.
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.
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?
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.
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 🙏🏻
