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- Scientific Consultation Companies
Single-Cell Technology that I can discuss about: -10X Genomics - Parse Bioscience - Honeycomb - BD Rhapsody - Mission Bio Spatial Technology that I can discuss about: - Visium (10X Genomics) - Nanostring Why you should have a scientific consultation with me? Because I am an expert in the field and I had a lot of failed experiments! So, I know what works and what will not. 😉 What about the payment? The payment will be done after the call. It will be charged accordingly to the minutes that will take.
- Consultations For Researchers
What is included? Advice and help on the following topics: EXPERIMENTAL DESIGN - Feasibility of the project - Best way of collecting/processing the samples - Best technology/approach to use for the project - Cost-reduction options TROUBLESHOOTING Find out the reasons why the experiments did not work. What should be changed and improved. SUPPORT MATERIAL -Links -Documents -Publications -Contacts Why you should have a scientific consultation with me? Because I am an expert in the field and I had a lot of failed experiments! So, I know what works and what will not. 😉 What about the payment? You will only have to pay me a coffee after our meeting. 😉
- Scientific Writing or Editing
What is included? -Writing the scientific sessions related with single-cell and spatial transcriptomics experiments. -Editing scientific sections related with single-cell and spatial transcriptomics experiments. -References What about the payment? This meeting will be free, to check if I can help you. We will discuss also the price. A final invoice will be send after the job is done. Prices Writing 0.20€/word Editing: 0.013€/word
Blog Posts (16)
- Mission Bio: Revolutionizing Single-Cell Genomics
In recent years, single-cell analysis has emerged as a game changer in the field of life sciences. It provides unprecedented insights into cellular heterogeneity and has the potential to change the way we diagnose and treat diseases. Mission Bio, a company funded in 2014, is at the forefront of this field, developing novel approaches to studying single-cell genomics. Their goal is to change the way scientists study disease at the single-cell level by enabling the detection of rare cell populations and identifying genetic mutations that contribute to disease. Mission Bio's areas of expertise include target high-throughput single-cell DNA analysis and multi-omics analysis. Their cutting-edge technology has the potential to transform the field of single-cell genomics, providing a level of resolution that traditional bulk sequencing methods cannot provide. The Tapestri Platform Mission Bio developed the Tapestri Platform to accomplish this goal. The Tapestri® Platform is a powerful tool that is increasingly being used for translational research and clinical trials at biopharma companies and in academia. This machine isolates and barcodes individual cells using microfluidics, allowing us to sequence the DNA of each cell separately. This provides a level of resolution that traditional bulk sequencing methods cannot provide. Applications of the Tapestri Platform Mission Bio offers a number of kits and protocols that can be used with the Tapestri platform (Table 1). This technology has a wide range of applications in the biosciences. One of the most significant applications is in precision medicine and molecular profiling of cancer samples, where the technology can be used to identify rare subclones that are resistant to therapy. This information can be used to develop more targeted therapies that are tailored to each patient's specific needs. The technology can also be used in immunology research to study the diversity and functionality of immune cells, in neurology research to study neuronal heterogeneity, and in the cell and gene therapy space, where the technology could be leveraged to detect Viral Vector Copy Number, as well as mono-allelic and bi-allelic edits in CRISPR edited cells, amongst many other applications. These are just a few examples of the power of this technology. In conclusion, Mission Bio is revolutionizing the field of single-cell genomics with its cutting-edge technology and solutions. If you're a scientist interested in studying single-cell DNA and immunophenotyping, the Tapestri Platform is an ideal tool to help you achieve your research goals. Be sure to explore more helpful content on their website, LindedIn, Twitter or in my podcast ( Episode 16: Mission Bio: single-cell targeted DNA & more). You can also contact Mission Bio team or Gema Fuerte, my guest at the podcast. Start using Mission Bio's technology today to discover unprecedented insights into cellular heterogeneity and improve patient outcomes. I hope this blog was useful for you. Thanks for reading it. Cheers, Cátia
- Single-Cell DNA Sequencing Methods
Single-cell DNA sequencing (scDNA-seq) is a powerful genomics tool that enables the detection of genetic variations at the single-cell level. It has revolutionized our understanding of genetic heterogeneity and disease development. In this blog, I will explore the various scDNA-seq technologies available and their applications in research and clinical settings. There are several techniques available for scDNA-seq, including whole-genome sequencing, targeted sequencing, DNA methylation sequencing, and chromatin accessibility assays. Whole-genome sequencing methods involve sequencing the entire genome of a single cell, providing comprehensive information about the genomic content of the cell. Several commercial solutions are available, including those offered by Qiagen (RepliG), Bioscryb (ResolveDNA), Merck (GenomePlex® Single Cell Whole Genome Amplification Kit or illustra™ Single Cell GenomiPhi™ DNA Amplification Kit ), Takara Bio (Pico PLEX® Single Cell WGA Kit), Silicon biosystems (Ampli1 WGA plus kit) or Yikon Genomics (MALBAC Single Cell WGA Kit). These low-throughput kits are all plate-based methods and should be used as a tool for discovery. However, caution is needed when using these methods. Ideally, DNA amplification should be stopped before the PCR plateau phase, as DNA amplification errors are more likely to occur after this point. Additionally, we need to be careful with DNA contaminations. Targeted sequencing focuses on specific genomic regions of interest, allowing for more sensitive and cost-effective sequencing. This technology should be used as a validation tool, as we must already have identified previously the genes we are interested in analyzing. Mission Bio offers a high-throughput droplet-based method, the scDNAseq kit. In addition to detecting DNA sequence alterations (e.g. single nucleotide polymorphisms, mutations, DNA rearrangements), with scDNA-seq technology we can also detect other DNA modifications such as DNA methylation or chromatin state modifications. DNA methylation is an epigenetic mechanism that regulates gene expression. It involves the addition of a methyl chemical group (-CH3) to certain DNA base pairs, most frequently to cytosines. Single-cell methylome sequencing allows us to study DNA methylation and its impact on gene expression. Some commercial available options include xGen™ Methylation-Sequencing DNA Library Preparation Kit (Integrated DNA Technologies), TWIST NGS Methylation Detection System (Twist Bioscience), or scTAMseq (Mission Bio). Here, most of the approaches are plate-based, with the exception of the last one from Mission Bio. Chromatin is nothing else than DNA wrapped around proteins (histones), forming a "bead necklace", the only way for our DNA to fit inside our cells nuclei. This necklace, chromatin, can have two states: relaxed (accessible) or condensed (closed). Relaxed chromatin indicates a high probability of gene expression at a certain region of the genome. To study chromatin accessibility, we can use scATAC-seq (single-cell sequencing assay for transposase- accessible chromatin) protocols. Basically, with the help of transposase enzymes that work like scissors, we will be able to cut only the relaxed regions of the chromatin, allowing us to know what DNA regions are being expressed at the single-cell level. Several kits are available for studying it, such as ICELL8 scATAC-seq (Takara Bio), scATAC-seq (10X Genomics) or SureCell ATAC-Seq Library Prep Kit (Biorad). These one are all droplet-based methods and consequently high throughput. ScDNA-seq techniques have a wide range of applications in both research and clinical settings. Researchers use these techniques to study the genetic heterogeneity of cancer cells, understand the development of early embryos, and investigate the genetic basis of various diseases. In clinical settings, single-cell DNA sequencing is being used for diagnostic purposes, such as the detection of rare cancer cells or the identification of genetic mutations associated with inherited diseases. Stay informed and up-to-date on the latest developments in scDNA-seq technology by listening to our (free) podcast. In case you don't find the information that you need, please contact me. I may be able to help. I hope this blog post was useful for you. Thanks for reading it. Cheers, Cátia
- Exploring the Three Categories of Single-Cell Methods
Biology has undergone a revolution thanks to single-cell studies, which have made it possible to examine cells with never-before-seen accuracy. It can be confusing with so many different protocols available. However, if we look at them closely, they can be divided into three main categories. I'll dive into each of these categories in this blog post. By the end of it, you will be better able to weigh the advantages and disadvantages of each method. 1. Plate-based Methods This was the first method to appear and be published. Cell isolation is done by placing one cell in one well. This can be done manually under the microscope or in an automated way using an automatic cell dispenser, or FACS. If using FACS, we can even do a simple multiomic approach. Prior to FACS, we stain our cells with one or more antibodies against the protein (s) of interest. After that, we will do index sorting. Basically, we will save the characteristics of each cell and the plate well where it is localized. After that, we will be able to correlate this information with the genomic or transcriptomics information of each cell. Example: Cell 1A is expressing protein B and has five apoptotic genes up-regulated. The essential material for this method are plates. They can be 96- or 384-well plates. Some commercial options available based on this type of method are: REPLI-g Advanced DNA Single Cell Kit (Qiagen), SMART-Seq Single Cell Kit (Takara Bio), ResolveDNA or ResolveOME (Bioscryb), or Evercode Whole Trancriptome (Parse Biosciences). With the exception of Parse Biosciences technology, plate-based approaches are low-throughput assays. So, if you have between a dozen and a hundred cells, you can use these approaches. 2. Micro, Nano, or Pico-based Methods Similar to the plate-based methods, here we also use wells to individualize cells. But in this case, the wells are very tiny. Depending on the commercial brand, we can have micro, nano, or pico-wells. These wells make part of a chip. After we load the cell suspension on the chip, the cells will fall by gravity into the wells. To be sure that we have one cell per well, we need to use the recommended cell concentration. This type of approach is a high-throughput assay, giving us the option of analyzing large numbers of cells. Some commercial options are: HIVE scRNAseq (Honeycomb Biotechnologies), GEXScope single cell RNA kits (Singleron), the ICELL8 system (Takara Bio) and BD Rhapsody system (BD Biosciences) This type of method is ideal in cases where we want to study sensitive cells, like granulocytes or neutrophils. The main reason is that the cells enter the wells by gravity, not due to forces that can make them "explode", what makes this type of method very gentle with the cells. Some commercial options even allow us to load our cells into the chip, store them, and perform the experiment days later. This can be crucial for projects where the sample collection site is different from the laboratory site or when the samples cannot be processed on the same day of collection. 3. Droplet-based Methods These are the most widely used and known single-cell methods. Some commercial options available are those from 10X Genomics (Chromium Controllers), Mission Bio (Tapestri), Dolomite Bio (Nadia), or MGI (DNBelab C Series). To use this type of assays, we will need a machine that will be able to individualize one cell inside an oil droplet. Just for you to have an idea of how it works, let's imagine a thin horizontal capillary or channel where we will load our cells that are resuspended in a water-based mixture formed by all the constituents needed for our downstream application (e.g., DNTP, enzyme, etc.). In the middle of the horizontal channel, there will be a vertical channel crossing it. In this one, there will be a flow of unique labels that are small beads. One bead will be attached to one cell. After the cell is labelled with the unique bead, it will continue in the horizontal channel flow until it enters a pool filled of oil. When this happens, it will be formed automatically an oil droplet around the cell, being this the way of isolating it from the others. These droplets resemble kitchen droplets when we mix water and oil. Each droplet will work as a PCR reaction tube. The droplet-based methods are high-throughput assays and they can be used in most part of the research projects. Since this type of method is the most developed, we will find more applications (e.g. genomics, transcriptomics, epigenomics, multiomics...). Clarification: Sometimes people refer to the droplet-based methods as microfluidics. It is true because the machines are based on a microfluidic system. However, microfluidics is also the base of the chips (micro, nano, or pico-well-based methods). So, microfluidics refers to systems that can process small quantities of fluids by using tiny channels with dimensions at the micro-scale. Now that you know the three main different types of single-cell methods, you can choose better the technology for you project. I hope you find this article useful. Have a lovely day. Cheers, Cátia 4 DAYS TO START Exploring the Cutting-Edge World of Single-Cell Technology An Introductory Course Tuesday, May 9 - Tuesday, July 182023
Other Pages (13)
- Recordings | Single Cell World
RECORDINGS Check my scientific recordings, free masterclasses and much more...everything about single-cell technology. Free Recordings All Categories Play Video Play Video 25:18 Market and Market talk_CM Talks to Markets & Markets Play Video Play Video 00:07 Catia Moutinho Sc to analyse mRNA isoforms Play Video Play Video 40:50 Advice For Life Scientists Applications of Single-Cell Class 2/2 | Unboxing the World of Single Cell Mini-course 60 minutes Play Video Play Video 50:40 Advice For Life Scientists What is single cell technology Class 1/2 | Unboxing the World of Single Cell Mini-course 60 minutes Play Video Play Video 00:40 Catia Moutinho scDNA companies Play Video Play Video 00:04 Catia Moutinho Single-Cell Methods Play Video Play Video 00:34 Catia Moutinho Single-Cell experiment that you didn't know about.... Play Video Play Video 00:33 Catia Moutinho Single-cell Plate Based Method Subscribe to The Single-Cell World Email Join Thanks for subscribing our website!
- Exploring the Cutting-Edge World of Single-Cell Technology: An Introductory Course
Exploring the Cutting-Edge World of Single-Cell Technology An Introductory Course Tuesday, May 9 - Tuesday, July 18 2023 Join Welcome! Let’s chat COURSE FEATURES ALL SCIENTISTS BEGINNER LEVEL SELF-PACED IN THIS COURSE WE WILL COVER... Single-Cell Omics You will discover the different types of single-cell omics, including genomics, transcriptomics, and proteomics. Single-Cell Sequencing Technology You'll learn about all technology approaches, focusing on commercial choices. Next Generation Sequencing You will learn about the basics of Next Generation Sequencing (NGS), an essential part of a single-cell experiment. Data Analysis You will get an overview and basic knowledge on the single-cell data analysis. CONTENT MODULE 1: Onboarding MODULE 2: Basics of Single-Cell Research MODULE 3: The Different Single-Cell Omics MODULE 4: Single-Cell Sequencing Methods MODULE 5: The Commercial Single-Cell Sequencing Technology MODULE 6: The Steps of a Single-Cell Experiment MODULE 7: Next Generation Sequencing MODULE 8: Data Analysis Essentials MODULE 9: Considerations to Plan Your Single-Cell Experiment MODULE 10 : Closing and Future Remarks WHAT TO EXPECT? Group Meetings Each Tuesday we will meet to talk about what you have learned and any questions you might have. These meetings are not mandatory . Recorded Classes Each Wednesday a new module with recorded classes will be released. Quizes Each week there will be a Quiz for you to test what you have learned. Certificate You should end this course in 2 months. However, if you cannot, you can take your time. The recorded classes and group meetings will be available for 1 year. THIS IS FOR YOU IF... you know what is a cell and its constituents you have basic knowledge on molecular biology you are a wet-lab or dry-lab researcher you are interested in single-cell sequencing technology THIS IS NOT FOR YOU IF... you don't know what is a cell you don't have basic knowledge on molecular biology no interest in single-cell sequencing technology THE TEAM Meet your instructors... Cátia Moutinho, PhD Course Director Ayoub Lasri, PhD Data Analysis Collaborator Sophie Wehrkamp-Richter Next Generation Sequencing Collaborator Cátia is a senior scientist with more than 20 years of experience in Cancer Biology, Epigenetics, Genomics and Single-Cell Technology. She holds a PhD, 2 master’s degrees, and many years in research as a group leader. Currently, she's a scientific consultant in the field of single-cell and spatial transcriptomics research. Also, she's the co-Founder of the following startups: Advice FLS , Mostly About Science and The Single-Cell World . Ayoub has expertise in bioinformatics and applied mathematics. He is the founder of Single-Cell Analytics, a biotech startup that uses single-cell data analysis to improve patient treatment and outcomes. He is also a member of several professional organisations and has several papers published in prestigious journals. Sophie is a Product Manager at Illumina – where she manages collaborations for single cell and spatial multiomics. Previously, she was working as an Applications Scientist to help Illumina customers troubleshoot their experiments. She holds a PhD in genetics from France and did a few postdocs at Scripps Research and UCSD, focusing on DNA repair. COURSE VALUED IN: 300 € What you will pay:10€ Why valued in 300 € ? Over 8 hours of recorded classes for extensive learning. 1 year access to course material to fully digest and understand content. Direct access to experts in the field for valuable feedback and insights. 100% support to help achieve learning goals with confidence. Up-to-date information provided for the latest and most relevant knowledge. Networking opportunities with other professionals in the field to build connections and open up career opportunities. Certification for demonstrating expertise and qualifications. Personal growth and fulfilment through learning new things and developing new skills. W hy only paying 10 € ? Everyone should have access to the basic information about single-cell technology. Scientific studies have shown that people will not complete a course if they are given free access to it. This fee is intended to secure your participation in the course. This funding, will contribute toward the cost of the online learning platform where we will publish the course. This investment will pay off in terms of career advancement, personal growth, and other benefits in the future. WILL YOU LOSE THIS OPPORTUNITY? Inscriptions will end May 7, 2023. After you will need to wait until we open a new call. Join Join our community! Join our email list and get our weekly newsletter with the latest news related to single-cell research and specials deals exclusive to our subscribers. Enter your email here Sign Up Welcome!
- Module 2: Basics of Single-Cell Research
Hi! Play the video for the class of module 2, basics of single-cell research. Any questions or doubts, please contact me by email: firstname.lastname@example.org or by WhatsApp: +351913900832 Here you can find the slides in PDF from this class. Feel free to download them. See you next week on our next Zoom Meeting. Cheers, Cátia