The Systems Biology of COVID-19 and the SARS-CoV-2 virus. The class will build a foundation that includes the emergence of complexity, simple biological subsystems, their reductionist and equivalent toy and organ-chip models, and the measurements required to specify model architecture and parameters. Applications to biology, physiology, medicine, chemical and biological defense, pharmacology, drug discovery, and toxicology. UGrad: PHYS 240 01 and BME 290B; Grad: PHYS 326 and BME 395C.
Friday, January 23, 2015
SysBio15 Asgn_7C_Class_07_Short Presentation_03_2015_01_27
Genomics: Review Short Presentation 03
Oliver_SP-RNAseq_01.22.2014.pptx. in the Student_Short_Presentations
folder in the VU-Box and figure out as much as you can on your own. Post
a PCRC on the Blog, focusing on what you want explained in more detail.
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James Pino
ReplyDeleteAsng 7C
0:Knew:Central Dogma of mol. bio.
1:Learned: Methods to find what RNA is transcribed.
2:Pressing: Is a single cell enough to RNA-seq? What quantities are needed? How fast is the process? Can you compare cells within a population? How long is RNA transcribed before it gets read/degraded? Just because the RNA is present does it always get transcribed?
3:Presentation: Possible a tutorial on using the software and what data looks like?
4:Thoughts: This makes me realize I need to know more about the time scales of RNA.
Kate Jones
ReplyDeleteAssignment 7C RNA-Seq
0. Knew: Basis of DNA-->RNA-->Protein via transcription and translation. I have also used sanger sequencing for DNA fragments.
1. Learned: The procedure and a few examples of applications of RNA-Seq
2. Pressing ?: Wouldn't a reliance on a base genome make this type of sequencing extremely limited? If the goal is to identify unknown variations, reliance on the original genome and known SNPs would the analysis. This is why microarrays are not the best method, but the table shows that RNA-Seq also relies on the base genome in cases.
3. Presentation: going through the comparison of transcriptomics methods and the pros and cons of different methods
4. Thoughts: I liked seeing the examples of applications of RNA-seq in recent publications
Juan Gnecco
ReplyDeleteAssignement 7C
0. knew: About RNAseq, some basics how it works and helped perform one before.
1.Learned: A good refresher on the different methods of RNA-seq along with their pros and cons.
Pressing: Could you discuss the differences in deep sequencing I always get that confused.
Is there an epigenetic-seq available yet? If not, then shouldn't any epigenetic methylation data be coupled with RNA-seq and additionally validated by protein levels?
3. Presentation: RNA-seq with examples of application (burtterflies)
4. Thoughts: Good use of an example of its use.
Juan Gnecco
ReplyDeleteAssignement 7C
0. knew: About RNAseq, some basics how it works and helped perform one before.
1.Learned: A good refresher on the different methods of RNA-seq along with their pros and cons.
Pressing: Could you discuss the differences in deep sequencing I always get that confused.
Is there an epigenetic-seq available yet? If not, then shouldn't any epigenetic methylation data be coupled with RNA-seq and additionally validated by protein levels?
3. Presentation: RNA-seq with examples of application (burtterflies)
4. Thoughts: Good use of an example of its use.
Arman Chowdhury
ReplyDeleteAssignment 7C
0. Knew: Mechanics of gene expression and protein synthesis
1. Learned: Different techniques exist for RNA sequencing – microarray and SAGE techniques. Application: Seasonal changes in butterfly wing phenotype can be understood using RNA-sequencing.
2. Pressing ?: Do you always need a reference point to figure out what you are looking for in a RNA sequence? Is there room for investigative exploration, for example detecting expression of a harmful mutation?
3. Presentation: Useful notes attached with slides. However, I hope presenter explains the mechanics of high-throughput sequencing technology in class.
4.Thoughts: The continually changing nature of the transcriptome of a cell is what makes RNA sequencing so exciting. The process of sequencing RNA seems to be like recording images of DNA’s complex activity frozen in time. It can be a tremendous research tool for understanding human physiology and pathology, for example for observing cellular activity in diseased state, and cancer proliferation etc.
Tim Lee
ReplyDeleteAsgn_7C
0. Knew: Basics of gene expression and protein synthesis.
1. Learned: What transcriptomics entailed. Different transcriptomics technologies and details about how some of these technologies work. Advantages of RNAseq over other technologies. Applications of RNAseq and creating libraries to map out transcription factors and expression.
2. Pressing: How long is the sequencing process? Could you explain the significance of aligning the data and where the reference sequence comes from?
3. Presentation: Transcriptomics and advantages of RNAseq technologies.
4. Thoughts: The idea of trying to sequence RNA expression and all of the applications of it seems so incredible to me. It's crazy to think how much sequencing there is to do though.
Cami Johnson
ReplyDeleteAssignment 7C: RNA seq
0. Knew: The central dogma of molecular biology: DNA --> RNA --> protein. Different methods for DNA sequencing, like the Sanger method.
1. Learned: How RNA sequencing works. Other sequencing techniques and their advantages and disadvantages. Why RNA sequencing is more advantageous to some applications than other methods.
2. Pressing ?: How long does RNA-seq take compared to other techniques? How do you get the reversible terminators to bind to the second base in the second chemistry cycle?
3. Presentation: examples of situations in which RNA-seq is used and no other technique would be suitable
4. Thoughts: The examples at the end of the presentation were really interesting. However, I think a more thorough explanation of the high-throughput sequencing technologies in class will help me understand the process better.
Priyanka Ravichandran
ReplyDeleteAssignment 7C
0. Knew - central dogma of molecular biology
1. Learned - RNAseq includes the observation of various things; learned about it's advantages relative to other techniques.
2. Pressing - Where does the reference sequence come from? How big of a RNA strand can be sequenced at a time? How long does this process take?
3. Presentation - overview of RNAseq
4. Thoughts - It was a very thorough presentation, providing background on why RNAseq used, step-by-step explanation of the process and the advantages of using it.
Shuaipeng "Jimmy" Zhang
ReplyDeleteAssignment 7C
0. Knew: Basics of transcription and gene expression.
1. Learned: RNA seq, and hybridization and sequence-based approaches. The advantages of RNA seq compared to tilting microarray and cDNA or EST sequencing.
2. Pressing ?: The presentation mentioned an article which addressed RNA as potential biomarkers. Are there any definitive RNA biomarkers? Still a little confused on the mechanisms of the different sequencing techniques.
3. Presentation: RNA seq and related sequencing techniques.
4. Thoughts: It was interesting to learn about the different types of sequencing and how they differ. That being said, is there anything which makes hybridization and cDNA sequencing superior to RNA seq? Or is everything about them obsolete.
Mark Vander Roest
ReplyDeleteAssignment 7C
0. Knew: Dogma of molecular bio and some associated biology.
1. Learned: Pros and cons of existing techniques and how RNAseq fits into that. How RNAseq works.
2. Pressing ?: Is there much risk in degrading RNA or missing sequences with a low copy number?
3. Presentation: RNAseq and quick overview of other techniques
4. Thoughts: Very digestible and well made presentation.
Zach Bednarke
ReplyDeleteAsgn 7c
Knew: very basic stuff
Learned: comparisons of various sequencing technologies as well as the outline of RNAseq.
Pressing ?: I don't understand how successive rounds of "chemistry" cause each nucleotide to fluoresce selectively. Am I understanding that part wrong?
Presentation: Comparing RNAseq to other technologies
Thoughts: I'm understanding the big picture but I have a lot of gaps I need filled when it comes to the actual process.
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ReplyDeleteChuck Herring
ReplyDeleteAsng 7C
0:Knew: Very basics about RNA.
1:Learned: The basics on how RNA-seq works.
2:Pressing: How well does RNA-seq correlate with protein expression levels?
3:Presentation: RNA-seq and similar technologies.
4:Thoughts: How are the cells prepped for RNA-seq? Are you limited to using cell lines?
0. Knew: Central dogma, basics of transcription, sanger sequencing.
ReplyDelete1. Learned: RNA seq and other sequencing methods. The advantages which make RNA seq valuable.
2. Pressing ?: What are RNA-seq's disadvantages (if any)? How difficult is reconstruction of the genome from fragmented sequences?
3. Overview of RNA-seq and how it improves on past methods.
4. Thoughts: Really well done presentation, very thorough and the images helped quite a bit to clarify. I still feel unclear on some things, but think seeing the presentation given will be very helpful for filling in the gaps.
Selene van der Walt
ReplyDeleteAssignment 7C
0. Knew: Sequencing is a very useful tool in various research areas, so that scientists can trace experimental results back to the actual changes in base pairs that are causing them.
1. Learned: About the specifics of RNA sequencing, I knew this was a method that existed but was unaware of the benefits it provides in terms of cost and time above other sequencing methods. I also got a brief overview about how the actual sequencing and amplification process works.
2. Pressing ?: I know that in my lab when we work with RNA it is very difficult because RNAses are so prevalent, is this a problem that occurs with RNAseq? If not how do they avoid it?
3. Presentation: Background of transcriptomics and RNAseq technology
4. Thoughts: An interesting presentation on an area I know very little about, it will be good to discuss in class and get a few more details about how the process actually works, that I was unable to figure out on my own.
Cameron Togrye
ReplyDeleteAssignment 7C / RNA Seq
0. Knew: The various 'alternative' uses for RNA in the cell (for example with miRNA in regulation and tRNA in transcription)
1. Learned: The mechanism by which high throughput sequencing is carried out.
2. Pressing: What is the purpose of the terminator for each chemical cycle in the high throughput sequencing process? If it is to ensure that the cluster isn't too long, wouldn't this process involve an extensive set of terminators constructed specifically for the RNA sequence of interest?
3. Presentation: Non-coding sequences of RNA
4. Thoughts: I'm interested to find out the degree to which various fluorescently tagged nucleotides can be resolved with current technologies of microscopy. Is this the rate limiting step?