Comparing GEXSCOPE® v3 and Chromium® GEM-X Single Cell 3′ Kit v4: Mouse Bone Marrow 22.10.20261’We compared microwell-based (Singleron GEXSCOPE RNA Library Kit v3, GEXSCOPE) and droplet-based scRNA-seq (10X Genomics® Chromium GEM-X Single Cell 3′ Kit v4, GEM-X) using mouse bone marrow. We evaluated:Library qualityCell recoveryDetection sensitivityCross-platform data correlationKey findingsAt matched UMI counts, GEXSCOPE detected 21–27% more genes.GEXSCOPE showed a lower percentage of mitochondrial reads.A higher percentage of GEXSCOPE reads mapped to exonic regions.Comparable cell type representation, with closely correlated global gene expression.Data from both platforms were integrated without substantial batch effects.Study designSample: Mouse bone marrowLibrary preparation platforms: Microwell-based (GEXSCOPE RNA Library Kit v3) and droplet-based scRNA-seq (Chromium GEM-X Single Cell 3′ Kit v4) single cell sequencing kitsData analysis: GEXSCOPE data with the CeleSCOPE® pipeline, GEM-X data with Cell Ranger. Quality control, normalization, principal component analysis and clustering for both datasets. Data were integrated with Harmony.Download the technical note Download the technical notePlanning your next single cell experiment? Check out the comparison data to find out more.DownloadFAQFAQ Comparing GEXSCOPE v3 and GEM-X Single Cell 3' Kit v4 What is the difference between microwell-based and droplet-based scRNA-seq? Both approaches partition single cells so that each cell’s RNA is tagged with a cell-specific barcode. GEXSCOPE loads cells onto a SCOPE-chip, where cells settle into individual microwells by gravity. Chromium GEM-X partitions cells on a microfluidic chip in droplets in an emulsion. This technical note compares the two workflows using the same sample. Can I combine Singleron and 10x Genomics data in one analysis? In this comparison, data from the two platforms integrated with Harmony without substantial batch effects, and cells from both platforms were interspersed within every cluster.10x Genomics and Chromium are trademarks of 10x Genomics, Inc.A post by Yingting WangYingting earned her PhD from the National University of Singapore, specializing in cell biology and tissue engineering. She has eight years of laboratory and commercial experience in single cell multi-omics, including roles in R&D, sales, technical support, and scientific communication.Check out our latest blog posts Learn more 26.10.07 Medium to high throughput single cell sequencing: A guide for different scRNAseq applications Medium and high throughput single cell RNA sequencing are two approaches to obtain single cell transcriptomic profiles. Here, we highlight the differences between medium and high throughput approaches and look at some examples that illustrate the benefits of both methodologies Read more 26.09.17 Cancer mRNA Vaccines: What Single Cell Sequencing tells us Three years after Katalin Karikó and Drew Weissman won the 2023 Nobel Prize for the mRNA base modifications that made COVID-19 vaccines possible, that same… Read more 26.07.28 Single Cell Sequencing in Aging Research: A Practical Guide Why Single Cell Resolution Matters in Aging No individuals age in the same way. And neither do different tissues and cell types. Single cell analysis… Read more
26.10.07 Medium to high throughput single cell sequencing: A guide for different scRNAseq applications Medium and high throughput single cell RNA sequencing are two approaches to obtain single cell transcriptomic profiles. Here, we highlight the differences between medium and high throughput approaches and look at some examples that illustrate the benefits of both methodologies Read more
26.09.17 Cancer mRNA Vaccines: What Single Cell Sequencing tells us Three years after Katalin Karikó and Drew Weissman won the 2023 Nobel Prize for the mRNA base modifications that made COVID-19 vaccines possible, that same… Read more
26.07.28 Single Cell Sequencing in Aging Research: A Practical Guide Why Single Cell Resolution Matters in Aging No individuals age in the same way. And neither do different tissues and cell types. Single cell analysis… Read more