Mentors at Your Benchside

• Single Cell Sequencing: Tips to Optimize Nuclei Extraction and Counting

  #114 — High-quality nuclei extraction is pivotal for many genetic and epigenetic studies, including single cell RNA-seq to describe transcriptomic profiles and gene expression dynamics and ATAC-seq to determine chromatin accessibility.But nuclei samples are extremely delicate and can be challenging to prepare and count. In this episode, we provide some practical tips to prepare high-quality nuclei extracts and tailor your extraction protocol to your sample. We also compare methods to count nuclei, assess their quality, and demonstrate how automated nuclei counting can improve your workflow.Check out the original article for a graphic that shows you the level of purity and quality you should aim for with nuclei extraction. [1] If you want to learn more about automated nuclei counting, download this free eBook. [2] Read this article to learn how to count cells quickly using fluorescence microscopy. [3] And to hear directly from DeNovix experts on nuclei counting, watch their webinar Optimizing Nuclei Extraction & Counting for Single Cell Sequencing. [4]Resources: 1. Single Cell Sequencing: Tips to Optimize Nuclei Extraction and Counting. Available at: https://bitesizebio.com/78877/optimizing-nuclei-extraction/2. Automated Counting of Isolated Nuclei. Available at: https://www.denovix.com/ebook/automated-counting-of-isolated-nuclei?utm_source=bitesizebio&utm_medium=technicalcontent3. Quick and Easy Automatic Cell Counting in 4 Steps. Available at: https://bitesizebio.com/30184/quick-easy-automatic-cell-counting/4. Optimizing Nuclei Extraction & Counting for Single Cell Sequencing. Available at: https://events.bitesizebio.com/optimizing-nuclei-extraction/room

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• Personal Advice on How to Respond to Criticism of Your Grant Proposal Reviews

  #113 — Learning how to respond to criticism is an unavoidable aspect of grant applications. Follow all instructions from funding agencies to avoid immediate rejection.This episode of Mentors At Your Benchside gives you some simple strategies to ensure you respond to criticism in a constructive and proportionate way.For example, identifying reviewers can help you tailor your responses, but don't mention them by name! Plus, using a two-column document to systematize the criticisms and responses is a great way to organize feedback and distance yourself emotionally from it.Hit play for more tips, check out the original article for links to helpful resources [1], and check out our complete guide to funding series for advice on getting your research funded—directly from a former NIH grant reviewer [2].Resources:1. Personal Advice on How to Respond to Criticism of Your Grant Proposal Reviews. Available at: https://bitesizebio.com/80095/respond-to-criticism/2. The Complete Guide to Funding I: How to Become an Expert at Getting Funded. Available at: https://events.bitesizebio.com/the-complete-guide-to-funding-i-how/join

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• Isoelectric Focusing: A Simple Way to Enhance Your Protein Separation

  #112 — Isoelectric focusing (IEF) is a powerful technique distinct from the more familiar SDS-PAGE, [1,2] tailored for separating proteins or peptides based on their isoelectric points (pI). [3]This method capitalizes on the migration of charged molecules through a stable pH gradient until they reach a zone where their net charge is zero, halting their movement.Essential to setting up an IEF experiment are the IPG strips, equipped with a pH-responsive gel, and the sample, often mixed with carrier ampholytes for efficient migration.IEF's utility spans various applications, from enhancing 2D-PAGE protein separations to analyzing post-translational modifications and preparing samples for mass spectrometry. [4]Discover more about how this technique can advance your research and streamline your experimental workflows.Resources:1. How SDS-PAGE Works. Available at: https://bitesizebio.com/580/how-sds-page-works/2. Isoelectric Focusing: A Simple Way to Enhance Your Protein Separation. Available at: https://bitesizebio.com/26811/isoelectric-focusing-separation-proteins-peptides/3. The Definitive Guide to pH, pKa, and pI. Available at: https://bitesizebio.com/9425/what-is-ph-pka-pi/4. Detecting Post-Translational Modifications. Available at: https://bitesizebio.com/49322/detecting-post-translational-modifications/

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• Top 10 Uses of Microbes in Biotechnology

  #111 — In this episode, we dive deep into the fascinating world of microbes and their revolutionary applications in biotechnology. From environmental solutions to breakthroughs in health and medicine, microbes hold the key to some of the most advanced scientific developments.Discover how these microscopic organisms are transforming industries and pushing the boundaries of what's possible in science and technology. We’ll explore the latest research and applications that are shaping the future.For an in-depth look at this topic, make sure to read the corresponding article on our website. [1] Dive into an application you almost certainly know about, yeast two-hybrid assays, [2] and check this article out to learn how to increase protein expression in plants. [3]Resources:1. Top 10 Uses of Microbes in Biotechnology. Available at: https://bitesizebio.com/48446/microbes-biotechnology/2. Split Ubiquitin Yeast Two-Hybrid. Available at: https://bitesizebio.com/25286/split-ubiquitin-yeast-two-hybrid/3. P19 to the Rescue: How to Increase Protein Expression in Agroinfiltration. Available at: https://bitesizebio.com/29964/p19-increase-expression-agroinfiltration/

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• Let’s Talk About Stats: Methods for Comparing Two Sets of Data

  #110 — Comparing two sets of data is a fundamental process in statistical analysis, crucial for drawing meaningful conclusions across various fields. Whether it's for determining the success of an intervention, understanding market trends, or validating scientific research, the need for comparison arises.This episode delves into the essence of data comparison, focusing on two prevalent statistical tests: the Student’s t-test and the Mann–Whitney U test. [1] Each test comes with its assumptions and applicability, making the choice between them critical depending on the nature of your data.Read our related article to learn more about comparing multiple datasets. [2]Resources:1. Let’s Talk About Stats: Methods for Comparing Two Sets of Data. Available at: https://bitesizebio.com/19298/comparing-two-sets-of-data/2. Let’s Talk About Stats: Getting the Most out of your Multiple Datasets with Post-hoc Testing. Available at: https://bitesizebio.com/19318/lets-talk-about-stats-getting-the-most-out-of-your-multiple-datasets-with-post-hoc-testing/

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