Depixus’ Post

Cell type identification is pivotal in understanding immune responses and disease mechanisms, yet it remains a primary challenge in single-cell RNA sequencing analysis. The g.nome® platform emerges as an indispensable tool for accelerating single-cell analysis, empowering researchers to characterize cell populations accurately and efficiently. By leveraging advanced bioinformatics methodologies and comprehensive reference datasets, g.nome allows users to bypass time-consuming pain points of scRNA-seq analysis and focus on the results, ensuring precise and efficient characterization of cells. Our researchers recently used g.nome to annotate 10,000 PBMCs from a healthy donor, achieving high accuracy and confidence in cell type differentiation. This case study demonstrates the platform’s potential to transform biomedical research and therapeutic development. Learn more: https://lnkd.in/gMekN4KT #scRNAseq #bioinformatics #precisionmedicine

🌟 I can't wait for this new webinar with Paramita Chatterjee PhD, MBA from the MC3M (Marcus Center for Cell Characterization and Manufacturing) as she delves into the cutting-edge work happening in the realm of cell therapy manufacturing and characterization 🚀 🔬 We are thrilled to host Dr. Chatterjee, who will illuminate how the center employs Single Cell RNA Sequencing (scRNA-seq) to dissect cellular mechanisms with unprecedented detail. 🧬 Dr. Chatterjee will share how their approach leverages scRNA-seq to unravel the heterogeneity and functionality of therapeutic cells, establishing disease-specific expression profiles. From clinical to pre-clinical human cells, they design tailored analytical pipelines to meet the unique demands of each sample and experiment, ensuring precise biological insights from single-cell omics data. 🗓️ Mark your calendars https://lnkd.in/g-QMijtR #CellTherapy #SingleCellOmics #TherapeuticCells #Biotech #Research #Webinar #10xGenomics #Science #Innovation

The SciLifeLab call for Clinical Technology Development Projects granted ten collaborative projects involving the SciLifeLab technology platforms and clinical researchers, with potential to advance #precisionmedicine. The Clinical Genomics platform is involved in three of the projects: 🔸 Malgorzata Lysiak (Clinical Genomics Linköping) – Nanopore sequencing for methylation-based diagnosis of brain tumors 🔸 Bianca Stenmark (Clinical Genomics Örebro) – Shotgun metagenomic sequencing in clinical diagnostics for rapid sepsis diagnosis 🔸 Robert Månsson Welinder (co-applicant Valtteri Wirta, Clinical Genomics Stockholm) – From cytogenetics to cytogenomics: Implementing high-fidelity-long-read-based genome sequencing in clinical routine to provide comprehensive characterization of complex cancer genomes

Scientists from DTU Health Tech and collaborators have developed a new innovative tool for detailed live imaging and analysis of how cells move and respond to chemical signals within a 3D environment that closely resembles human tissue. The technology holds great promise for advancing our understanding of cancer and potentially other diseases by providing a more accurate simulation of the cellular microenvironment. "In a microfluidic device, we can create and control pH gradients similar to those found around solid tumors. The device’s unique design permits the subsequent detailed studies of cell behavior and gene expression after the initial experiments. Based on a reversible sealing, it allows to retrieve the cells after they have been exposed to a pH gradient. Together with a newly developed spatial transcriptomics workflow, it has the unique ability to capture the entire gene expression profile in relation to the varying pH levels", Associate Professor Rodolphe Marie explains. The work is a collaborative effort between scientists from DTU - Technical University of Denmark, Københavns Universitet - University of Copenhagen, and Bundesanstalt für Materialforschung und -prüfung, and is published in Science Advances. Read the full paper here: https://lnkd.in/gA-N-Nd8 #healthtech #microfluidics Jamie Auxillos, Roxane Crouïgneau, Yanfang Li, Yifan Dai, Arnaud Stigliani, Isabella Tavernaro, Ute Resch-Genger, Albin Sandelin, Stine F. Pedersen

🔬 When the impossible becomes possible🧬 Introducing the LUTHOR HD kit, the cutting-edge world of High-Definition Single-Cell RNA Sequencing (HD scRNA-Seq). 🌐 Overview: HD scRNA-Seq captures every mRNA, even those with less than 10 copies, offering a comprehensive view of each cell's transcriptomic status. 🛠 LUTHOR HD Kit: -Technology: RNA-amplification-based, ensuring detection of virtually every mRNA molecule. -Primer Usage: Utilizes oligo(dT) primers for 3' end mRNA-Seq. -Sample Input Range: Remarkable flexibility, from 1 ng to 10 pg (equivalent to 100 cells to 1 cell) and even lower, e.g., 1 pg with cytoplasmic extracts. -Sensitivity: Unparalleled sensitivity, detecting the majority of expressed genes at only 1 M read depth. 👩🔬 Applications: -Detailed cell subpopulation analysis after larger screenings (bulk scRNA-Seq). -Rare cell RNA analysis, including circulating tumor cells (CTCs) and innate lymphoid cells (ILCs). -Subcellular RNA analysis. -Single nucleus RNA-Seq. ⚛️ Conclusion: LUTHOR HD transforms single-cell RNA sequencing, offering an advanced toolkit for researchers to explore the intricate world of subcellular transcriptomics. 📊 Data and Details: the application note published in nature methods right here : https://lnkd.in/dhfnUwM6 #singlecell #rnaseq #LUTHORHD #transcriptomics #research #innovation

Researchers at the Cleveland Clinic have leveraged machine learning and multi-omics to uncover potential therapeutic targets for #Alzheimer’s disease (AD) by examining the gut-brain axis. Their study, published in Cell Reports, identified novel drug targets through the interaction between gut microbial metabolites and cellular receptors. https://cle.clinic/4cmuLYl Key findings include: 1. Machine Learning and Multi-Omics Approach: The researchers analyzed over a million potential interactions between gut metabolites and human G-protein-coupled receptors (GPCRs) using AI. This led to the discovery of previously unknown "orphan" GPCRs that may play a role in AD. 2. Experimental Validation: Lab experiments confirmed that metabolite agonists for these identified GPCRs reduced pathologically phosphorylated tau protein in AD neurons derived from stem cells. 3. Potential Targets: Notably, agmatine and phenethylamine, two gut metabolites, were found to interact with specific GPCRs (e.g., C3AR) and reduce tau hyperphosphorylation, a marker of AD.

🔬 𝐄𝐱𝐩𝐥𝐨𝐫𝐢𝐧𝐠 𝐭𝐡𝐞 𝐅𝐮𝐭𝐮𝐫𝐞 𝐨𝐟 𝐌𝐞𝐝𝐢𝐜𝐢𝐧𝐞: 𝐒𝐢𝐧𝐠𝐥𝐞 𝐂𝐞𝐥𝐥 𝐆𝐞𝐧𝐨𝐦𝐢𝐜𝐬 𝐚𝐧𝐝 𝐏𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬 𝐃𝐨𝐰𝐧𝐥𝐨𝐚𝐝 𝐒𝐚𝐦𝐩𝐥𝐞 𝐏𝐃𝐅: https://lnkd.in/gHVzsSwG Single-cell genomics is a method for examining the heterogeneity of cells and identifying new molecular characteristics concerning the clinical results. This strategy assists in allowing the complexity of cell variety to be identified in a sample without the loss of data that occurs when analyzing multicellular or bulk tissue samples. Single-cell genomics involves sequencing the DNA or RNA of individual cells. This technique helps in identifying genetic variations and understanding how different cells contribute to the function of tissues and organs. It has applications in cancer research, developmental biology, and understanding genetic diseases. Single-cell proteomics focuses on analyzing the protein content of individual cells. Unlike DNA or RNA, proteins cannot be amplified, making this a challenging field. However, advancements in mass spectrometry and sample preparation techniques have made it possible to study proteins at the single-cell level. This helps in understanding cell signaling, identifying rare cell types, and investigating disease mechanisms 1. Cancer Research 2. Developmental Biology 3. Neuroscience 4. Immunology 5. Stem Cell Research 6. Microbiology 7. Cardiovascular Research 𝐆𝐞𝐭 𝐌𝐨𝐫𝐞 𝐈𝐧𝐟𝐨: https://lnkd.in/g27MV_Wv 𝐊𝐞𝐲 𝐏𝐥𝐚𝐲𝐞𝐫𝐬: Illumina Thermo Fisher Scientific BD 10x Genomics Bio-Rad Laboratories Agilent Technologies QIAGEN PerkinElmer Abbott Merck Celsee, Inc. GENEWIZ from Azenta Life Sciences AstraZeneca Sartorius Promega Corporation Danaher Corporation #singlecellgenomics #singlecellsequencing #genomesequencing #scgenomics #singlecellanalysis #singlecell #nextgenerationsequencing #genomics #transcriptomics #molecularbiology #cellbiology #genetics #bioinformatics #singlecellrna #precisionmedicine #personalizedmedicine #functionalgenomics #singlecellresearch #genomicresearch #cellsequencing #singlecelltranscriptomics #crispr #scRNAseq #biotechnology #genomicsresearch #highthroughputsequencing #cellularheterogeneity #singlecelltechnology #omics

https://lnkd.in/gdeQS2b3. " Whiting School of Engineering Johns Hopkins School of Medicine Johns Hopkins Biomedical Engineering Johns Hopkins Biomedical Engineering Research Research Areas Immunoengineering Immunoengineering harnesses the power of the immune system to treat diseases such as cancer and promote tissue regeneration and healing. Education in Immunoengineering Our curriculum trains students at the molecular, cellular, and systems levels. Particular emphasis is placed on novel materials and methods to harness the body’s immune system to fight disease, and to promote tissue repair and healing. Students develop new biomaterials, vaccines, therapeutics, and systems to understand immune cell function and guide immune cell behavior. Research in Immunoengineering Our students and faculty are pioneering immunoengineering approaches to augment tissue regeneration, and to treat cancer and other diseases. Key research areas include: Biomimetic Materials We are controlling the signals that regulate immune cell responses at the macro and nanoscale through biomimicry and advanced materials design. Regenerative Immunology and Aging We are innovating platforms that modulate innate and adaptive immune responses to promote tissue regeneration and wound healing. We are investigating the impact of aging on the immune system and its function in repair and disease. Immuno-Oncology We are innovating platforms that modulate immune responses to potentiate vaccine efficacy, enhance drug delivery systems, and improve cancer treatment. Host Defense We are designing new material and cell-based therapies for correcting improper immune response, in the case of attack against self and autoimmune disorders, or for augmentation, in the case of ridding the body of foreign invaders. Systems Immunology and Computational Immunoengineering We are investigating how immune cells connect with each other and tissues to exert their functions. We are building systems models of cell and tissue function to provide insights that guide experimental and translational studies, and utilizing bioinformatics for improved neoantigen discovery. Molecular Engineering We are redesigning natural proteins and creating entirely new proteins as tools to both understand and manipulate the immune response. We are inventing biotechnologies to direct immune cell function. Synthetic Biology We are designing, fabricating, and integrating new biological components, ranging from individual molecular players such as proteins to cell-based platforms." 👇

📣 We’re excited to introduce Keara, an associate scientist at Virica and host of our new Ask the Virologist series! ✔ Here’s a quick video to learn a little bit about her background and what we do here at Virica. 💡 Leveraging our expert team and years of experience, we're excited to spark engaging scientific dialogue through our Ask the Virologist series. 👉 DM us with feedback, questions or add to the discussion! Some questions we have recently received: Question from Ramon Mendoza: “What are the product-related and process-related impurities that impact transduction efficiency? Are there attributes one can measure which would help predict transduction efficiency in primary cells when titre is established in a different well established cell line?” A: This is a really interesting question! Some process impurities that may impact transduction efficiency: ◾ Contaminating cellular free DNA in the final product can activate the interferon pathway, reducing transduction efficiency. DOI: 10.3390/cells12050732. ◾ There are indications that variations in the vector membrane lipid profile can alter vector transducibility and function. Further, the producer cell used to generate the vectors may cause these variations. Therefore, membrane lipidomics may be an interesting metric. Here are a few papers to check out: **https://lnkd.in/dGpeCbUG. https://lnkd.in/d3k548a9 **https://lnkd.in/dWRT4s68 ◾ Presence of empty capsids or partially full capsids may necessitate higher quantities for effective transduction. Quantifying full/empty capsid ratios can be useful for addressing this. ◾ Specific glycoproteins used in transduction can impact efficiency; for instance, standard VSV-G may not be optimal for certain cell types like NK cells due to receptor expression differences. DOI: 10.3389/fimmu.2019.02873 Using model-cell lines for viral titer versus transducing primary cell lines: ◾ Using immortalized or cancer cell lines introduces genetic variations, potentially affecting sensitivity to impurities. For example defects in antiviral pathways in model cell lines may not reflect those in target cells, affecting transduction outcomes. ◾ Understanding the impurities and vector design implications above can help bridge the gap between model cell systems and target cells. DOI: 10.1016/j.cellsig.2005.10.008 Question from LAURA BELMAR “How do you do your payload analytics, and have you considered using mass photometry for in process quality assessment?”. A: Great question! This relates to some of the characteristics listed in the above question. Certainly full/empty ratios can be assessed in this way and is a technique that can work across all varieties of custom/standard viral serotypes! DOI: 10.3390/ijms241311033 #virology #AskaVirologist #biomanufacturing #cgtreads

I'm helping our team at Virica Biotech share the mysteries of viral vectors with our new series! 🌟 Our small molecule enhancers integrate with any viral vector production platform (yes ANY). This versatility allows us to explore a diverse array of viral vectors and production processes within our lab, keeping me endlessly engaged and inspired. But with great diversity comes great complexity. We understand the challenges viral vector production can present. That's why we're looking to share our insights and expertise with you. All the wins and lessons we have learned in our journey. Do you have burning questions about viral vectors? Drop me a DM. #ViralVectors #Biotech #Biomanufacturing