iBiology Techniques
iBiology Techniques
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Next Generation Sequencing 2: Illumina NGS Sample Preparation - Eric Chow (UCSF)
www.ibiology.org/techniques/next-generation-sequencing
Next generation sequencing allows DNA samples to be sequenced quickly and affordably. Learn how next gen sequencing works and get tips on preparing and running your samples.
In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours! In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection.
In his second talk, Chow discusses Illumina NGS Sample Preparation. He goes over DNA and RNA preparation, bead-based (Ampure or SPRI) cleanups, and sample quantification and quality control.
And in two short how-to videos, Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.
00:00 - Start
00:36 - Review of next generation sequencing
02:13 - DNA library preparation
07:17 - RNA library preparation
14:26 - Bead-based cleanups
18:22 - Sample quantification and quality control
Speaker Biography:
Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.
Переглядів: 153 094

Відео

Single Cell Sequencing - Eric Chow (UCSF)
Переглядів 234 тис.3 роки тому
www.ibiology.org/techniques/single-cell-sequencing Dr. Eric Chow gives an overview of single cell sequencing, explains why this approach is useful, and talks through the leading methods. Single cell sequencing, as the name implies, allows researchers to examine the genomic information for individual cells. This provides an opportunity to examine cell-to-cell differences and identify cell subtyp...
Metadata in BioImaging - Jason Swedlow (U. Dundee)
Переглядів 3,6 тис.4 роки тому
www.ibiology.org/techniques/metadata Jason Swedlow explains what constitutes image metadata, and provides examples on how to catalog, organize, analyze, and share the metadata of biological images. In order to understand an image of a biological sample and what it represents, one needs to understand its metadata. Metadata is the information behind the image that shows the experimental procedure...
Multi-Dimensional Microscopy Datasets - Loic Royer (CZ Biohub)
Переглядів 4,2 тис.4 роки тому
www.ibiology.org/techniques/multi-dimensional-microscopy-datasets Modern microscopy produces large multi-dimensional datasets, which creates new challenges for data storage, processing and visualization. In this talk, Dr. Loic Royer uses a developing drosophila melanogaster embryo to explain how to solve some of the challenges produced by multi-dimensional microscopy datasets. Speaker Biography...
Bioimage Analysis 6: Tips and Best Practices (Anne Carpenter and Kevin Eliceiri)
Переглядів 2,8 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Bioimage Analysis 3: Segmentation (Anne Carpenter)
Переглядів 34 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Bioimage Analysis 4: Tracking (Kevin Eliceiri)
Переглядів 3,5 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Bioimage Analysis 5: Measurement and Phenotype Classification (Anne Carpenter)
Переглядів 7 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Bioimage Analysis 2: Pre-Processing (Kevin Eliceiri)
Переглядів 10 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Image Acquisition for Quantitative Analysis - Nico Stuurman (UCSF)
Переглядів 10 тис.4 роки тому
www.ibiology.org/techniques/image-acquisition Nico Stuurman provides an overview of the different tools, equipment, and software available to acquire an image of a biological sample, and the considerations one needs to take when using these tools. How do we visualize biological samples? In this talk, Dr. Nico Stuurman provides an overview of the different tools, equipment, and software availabl...
Bioimage Analysis 1: The Basics: Getting Started (Anne Carpenter and Kevin Eliceiri)
Переглядів 9 тис.4 роки тому
www.ibiology.org/techniques/bioimage-analysis In this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re rea...
Bioimage Analysis - Christian Tischer (EMBL)
Переглядів 12 тис.4 роки тому
www.ibiology.org/techniques/introduction-to-bioimage-analysis Dr. Christian Tischer walks us through the main concepts of a typical bioimage analysis workflow and explains how to quantitatively interpret the content of microscopy images. Microscopy is a key technology driving biological discovery. Nowadays, microscopy based scientific findings must be substantiated by quantitative image analysi...
iBiology Bioimage Analysis Course - Life cycle of an image data set
Переглядів 4,5 тис.4 роки тому
www.ibiology.org/online-biology-courses/bioimage-analysis-course This course is designed as a graduate student level introduction to bioimage analysis and will provide an overview of the practice and principles of microscopy digital image handling. This series follows the life cycle of an image data set, from acquisition to analysis. It teaches important concepts and best practices, and provide...
The Scientific Community Image Forum - Anne Carpenter and Kevin Eliceiri
Переглядів 5 тис.4 роки тому
www.ibiology.org/techniques/scientific-community-image-forum The Scientific Community Image Forum is an online resource that helps scientists answer their bioimage analysis questions. In this talk, Dr. Anne Carpenter and Dr. Kevin Eliceiri encourage scientists to use the Scientific Community Image Forum when they have image analysis difficulties, and to familiarize themselves with the different...
ImageJ - Kevin Eliceiri (U. Wisconsin)
Переглядів 14 тис.4 роки тому
www.ibiology.org/techniques/image-j In this talk, Dr. Kevin Eliceiri provides an overview of ImageJ, explains how ImageJ has evolved through time, and demonstrates major functionalities of this open-source software. Since 1987, different versions of ImageJ have been used by scientists to analyze biological images. Speaker Biography: Dr. Kevin Eliceiri is an Associate Professor of Medical Physic...
CellProfiler - Anne Carpenter (Broad Institute)
Переглядів 13 тис.4 роки тому
CellProfiler - Anne Carpenter (Broad Institute)
Mass Cytometry Introduction - Susanne Heck (NIHR BRC)
Переглядів 26 тис.5 років тому
Mass Cytometry Introduction - Susanne Heck (NIHR BRC)
Imaging Flow Cytometry: A Brief Overview - Andrew Filby (Newcastle U.)
Переглядів 44 тис.5 років тому
Imaging Flow Cytometry: A Brief Overview - Andrew Filby (Newcastle U.)
Next Generation Sequencing 3: Purifying DNA Samples with Magnetic Beads - Eric Chow (UCSF)
Переглядів 49 тис.5 років тому
Next Generation Sequencing 3: Purifying DNA Samples with Magnetic Beads - Eric Chow (UCSF)
Next Generation Sequencing 1: Overview - Eric Chow (UCSF)
Переглядів 453 тис.5 років тому
Next Generation Sequencing 1: Overview - Eric Chow (UCSF)
Next Generation Sequencing 4: Checking Nucleic Acids with an Agilent BioAnalyzer - Eric Chow (UCSF)
Переглядів 63 тис.5 років тому
Next Generation Sequencing 4: Checking Nucleic Acids with an Agilent BioAnalyzer - Eric Chow (UCSF)
Visual Communication in Biology 2: Animating Molecular Biology, Part I - Janet Iwasa (U. Utah)
Переглядів 3,7 тис.5 років тому
Visual Communication in Biology 2: Animating Molecular Biology, Part I - Janet Iwasa (U. Utah)
Visual Communication in Biology 3: Animating Molecular Biology, Part II - Janet Iwasa (U. Utah)
Переглядів 5 тис.5 років тому
Visual Communication in Biology 3: Animating Molecular Biology, Part II - Janet Iwasa (U. Utah)
Visual Communication in Biology 1: Introduction - Janet Iwasa (U. Utah)
Переглядів 28 тис.5 років тому
Visual Communication in Biology 1: Introduction - Janet Iwasa (U. Utah)
Single-Cell Imaging and Reconstructing Mouse Development - Philipp Keller (Janelia/HHMI)
Переглядів 12 тис.5 років тому
Single-Cell Imaging and Reconstructing Mouse Development - Philipp Keller (Janelia/HHMI)
FACS - Fluorescence Activated Cell Sorting - Steffen Schmitt (DKFZ)
Переглядів 26 тис.5 років тому
FACS - Fluorescence Activated Cell Sorting - Steffen Schmitt (DKFZ)
Flow Cytometry Introduction - Malte Paulsen (EMBL)
Переглядів 115 тис.5 років тому
Flow Cytometry Introduction - Malte Paulsen (EMBL)
Synthetic Biology: Realizing synthetic carbon dioxide fixation - Tobias Erb
Переглядів 18 тис.6 років тому
Synthetic Biology: Realizing synthetic carbon dioxide fixation - Tobias Erb
Synthetic Biology: Engineering bacteria with CRISPR - David Bikard
Переглядів 23 тис.6 років тому
Synthetic Biology: Engineering bacteria with CRISPR - David Bikard
Synthetic Biology: Synthetic Biology and Escherichia coli - Steve Busby
Переглядів 11 тис.8 років тому
Synthetic Biology: Synthetic Biology and Escherichia coli - Steve Busby

КОМЕНТАРІ

  • @randnorberg4518
    @randnorberg4518 День тому

    RIP roger. May your legacy continue to fluoresce.

  • @SwanOnChips
    @SwanOnChips День тому

    Both the removal of scaffolding and the protein insertion machines as well as all the other unnamed irreducible complexity and interdependencies scream out Wonderfully Designed. Yet without any scientific evidence or explanation attributes their existence to the god of the evolutionary gaps, 'it evolved'. Has anyone ever explained a naturalistic process that could actually engineer this - or do we really have to rely on that oft repeated story?

  • @GiangTran-u6s
    @GiangTran-u6s 2 дні тому

    Thank you very much for the tutorial! Can it be used for detecting cells in 3D images?

  • @ArtAutumn
    @ArtAutumn 4 дні тому

    Isn't there a mistake on 9:27? I think the Fourier image should be rotated on 90 degrees, coz in the direction of x there are many freaquences due to sharp steps.

  • @Hiblackman
    @Hiblackman 6 днів тому

    Very interesting about nothing.

  • @alankhalil1646
    @alankhalil1646 12 днів тому

    great video. I needed this!

  • @chemistmashwani483
    @chemistmashwani483 13 днів тому

    sir i need a little help in selecting probe for my research can u please help me by ur kind suggestion

  • @zerdofish9989
    @zerdofish9989 16 днів тому

    FACS sorting hehe

  • @harishv7245
    @harishv7245 17 днів тому

    Great explanation professor

  • @gamertcell8425
    @gamertcell8425 17 днів тому

    The very first virus

  • @terpichore7667
    @terpichore7667 20 днів тому

    This was crummy. There are many logical gaps in the presentation. E.g., it is not clear how clusters have the same sequence. There are other UA-cam videos on NGS that are clearer.

  • @durgaprasadhembram9662
    @durgaprasadhembram9662 21 день тому

    Great explanation 👌

  • @CalvinGhasemi
    @CalvinGhasemi 23 дні тому

    I found this video very interesting. I have experience with mass spectrometer (LCMS) but this was interesting as it uses a similar principle.

  • @laxmidevi-rf9qj
    @laxmidevi-rf9qj Місяць тому

    kon kon class 8 me h or kis kis ko ye video goggle se mila h like karo

  • @kenschwarz8057
    @kenschwarz8057 Місяць тому

    What a revelation! That Huygens figured out the fundamentals in 1690 is also mind-blowing. Thank you for this fascinating presentation. It utterly changed the way I think about light and optics.

  • @makemyburdenlight
    @makemyburdenlight Місяць тому

    Can someone help me? I read a study that said they "looked at the various forms of the gene coding for a vasopressin receptor" among various people. Does that mean they only looked at active genes, or inactive ones as well?

  • @JamesVestal-dz5qm
    @JamesVestal-dz5qm Місяць тому

    How can you quantitate your images is vitally important because cellular processes are governed by the laws of physics. To help people with biology we need a physically accurate picture of the cell. Fluorescence excitation causes changes in the eigenstate of the electronic energy levels of the excited molecules, which can result in radiation that changes the state of neighboring molecules. However, fluorescence excitation still remains a powerful tool for measuring the rates of cellular processes. Dr. Dray always concludes her videos with sunscreen and subscribe because all humans are in a race against time to slow down the dynamics of radiation causing protein and DNA mutation in their cells.

  • @cary3345
    @cary3345 Місяць тому

    Skip to 14:00 if you just care about microscope

  • @jeannelorraineamponin6822
    @jeannelorraineamponin6822 Місяць тому

    I just want to say that you're a great teacher! Passing on not only knowledge but also the passion!

  • @BruinChang
    @BruinChang Місяць тому

    Thanks a lot to give this presentation!

  • @victoronuche2405
    @victoronuche2405 Місяць тому

    How do i import images on cellprofiler and how can i get a software that works on windows 7

  • @Andrea-sh9sn
    @Andrea-sh9sn Місяць тому

    Thanks a lot. What would happen if instead of putting 5% PhiX in the cartridge, I mistakenly put more amount (60%). And I put the correct amount from the library?

  • @user-ec6mo4sj4z
    @user-ec6mo4sj4z Місяць тому

    amazing lifesaver

  • @esan120au
    @esan120au Місяць тому

    Thanks so much! Even the illumina webinar was not as clear as your presentation! 👏👏👏👏

  • @Me-ld8bt
    @Me-ld8bt Місяць тому

    Thank you for the great explaination!

  • @nia2121
    @nia2121 Місяць тому

    this is great!

  • @ggk9828
    @ggk9828 Місяць тому

    Is it safe then to assume that molecules that divide would be the point at which inorganic becomes organic and chemistry becomes biology?

  • @esan120au
    @esan120au Місяць тому

    Thanks. Can you clarify at 8:04 when you said each beads has many barcoded oligo-dT oligos on its surface. What is the scale of this "many"? Millions? Are these supposed to attach to the entire transcriptome of a cell?

  • @esan120au
    @esan120au Місяць тому

    17:13 quantifying proteins using DNA sequencing (CITE-Seq) 21:26 universal antibodies for a universal cell-surface protein that have unique barcodes for each cell to detect the unwanted doublets (droplet with one bead but two cells)

  • @dbs5817
    @dbs5817 Місяць тому

    Awesome

  • @jameskellinger8314
    @jameskellinger8314 Місяць тому

    What is the purpose of waving your hands?

  • @jameskellinger8314
    @jameskellinger8314 Місяць тому

    Please don't wave your hands--it is very distracting

  • @mervatel-deftar8412
    @mervatel-deftar8412 2 місяці тому

    Amazing overview Excellent

  • @chepai1827
    @chepai1827 2 місяці тому

    Nice talk!

  • @JH-it2yr
    @JH-it2yr 2 місяці тому

    Very detailed and clear! No ads interrupting! Thank you very much professor!

  • @ylidene6222
    @ylidene6222 2 місяці тому

    Thank you! It helped me a lot

  • @user-il4jz8mu6o
    @user-il4jz8mu6o 2 місяці тому

    I looking for good videos in how analyzing the a dataset of Peripheral Blood Mononuclear Cells (PBMC) ?? Thank you

  • @1point689
    @1point689 2 місяці тому

    fourier transfer of fourier himself is such a nerd thing to do lol, love this lecture Thanks!

  • @1point689
    @1point689 2 місяці тому

    Great lecture!

  • @kalyanirajalingham1286
    @kalyanirajalingham1286 2 місяці тому

    Fantastic video! You explain very well

  • @user-ci7fe1jj8x
    @user-ci7fe1jj8x 3 місяці тому

    روى ابن ماجه وغيره أن النبي صلى الله عليه وسلم قال: إن مما يلحق المؤمن من عمله وحسناته بعد موته علما علمه ونشره، وولدا صالحا تركه، أو مصحفا ورثه، أو مسجدا بناه، أو بيتا لابن السبيل بناه، أو نهرا أجراه، أو صدقة أخرجها من ماله في صحته وحياته تلحقه بعد موته. m.ua-cam.com/video/-qgsOvwlK0w/v-deo.html&pp=ygUg2KfZhdis2KfYr9mG2Kcg2LnZhdix2Ygg2YXYrNiv2Yk%3D

  • @exciton007
    @exciton007 3 місяці тому

    Thanks for this great presentation!

  • @loreenzo2120
    @loreenzo2120 3 місяці тому

    how does this not have more views

  • @prabhatmishras421
    @prabhatmishras421 3 місяці тому

    Best lecture

  • @thehumanconvergence
    @thehumanconvergence 3 місяці тому

    Great stuff, will be featuring you in our next episode!

  • @wilsonfrantine
    @wilsonfrantine 3 місяці тому

    If you are really interested on, u can dive in Jost 2018 (measuring differentiation). He argue about the limitations of Fst and its relative statistics (yes, there's a lot). You will see that comparing expected heterozygosity as a proxy of differentiation might fail at the populational level in several occasions. For instance, it can only reaches 1 if there are no allelic sharing, and put 11% of differentiation when there are 35% of allelic differences because it rely on the average of a possible heterozygosity that might comes from a loci in case of panmixing breeding (a lot of assumptions). Jost argue that it would be more helpful try to compare the frequency of alleles, mainly for those loci (or markers) that can measure a multialellic state ( more than two, usually). Fst still usefull, but you can't take that as the ultimate tool to measure everything. Remember, a 30 inch ruler is useless to measure the distance between the sun and the earth or the circumference of a cell.

  • @wemcal
    @wemcal 3 місяці тому

    Great video and great information

  • @aminchy01
    @aminchy01 3 місяці тому

    Great to hear

  • @thisumamarasinghe8171
    @thisumamarasinghe8171 3 місяці тому

    talking bullshit

  • @luisfernando-mm3jt
    @luisfernando-mm3jt 3 місяці тому

    Nice work