How we tackle cell type annotation
One of the main challenges in single-cell data interpretation is annotating cell types. In this blog, we explain our process of collaborating with clients to analyze single-cell data and assign cell type identity labels.
How we identify a cell
Cell type identification is currently one of the leading applications of single-cell RNA sequencing experiments. How do we do it? In this blog, we zoom in on the nine-step process that takes you from raw sequencing data to assigning cell type labels.
Is 10x Genomics suitable for my project?
10x Genomics solutions may or may not be suitable for your project, depending on your sample type and your number of cells. How do you know?
How to start with 10x Genomics
In the world of single-cell RNA sequencing, 10x Genomics has made a name for itself as a leading provider of high-throughput solutions. But for those new to the field, the prospect of starting with 10x Genomics solutions can be intimidating. That’s why, in this blog post, we’ll show you how to take the first step….
What is a UMAP plot?
Single-cell papers usually show their data in the shape of the UMAP plot. What is it?
What does a t-SNE plot show?
You can find a t-SNE plot in almost every single-cell paper. What are the dots, colors, and axes? Learn how to interpret the plot.
CITE-seq: single-cell RNA sequencing plus surface protein analysis
CITE-seq is a method to simultaneously perform single-cell RNA sequencing and single-cell surface protein analysis. But how does this work? And what does it accomplish?
Three reasons to start small with single-cell sequencing
When you first start with single-cell sequencing, it’s often best to start small with a pilot project. Here, we explain why. We updated this blog from March 2021 on 5 December 2022. We rewrote it and included a company comparison as a reason to start with a pilot project. Technical and biological validation If you start a…
What is t-SNE?
One of the most recognizable figures in a single-cell paper explained simply. What is it? What is its purpose? And how does t-SNE work?
How to get started with single-cell data analysis
Once you receive your single-cell sequencing data, you can get started with your single-cell data analysis. It can be overwhelming when you first download the data. Here, we’ll give you some tips for the first steps of single-cell sequencing data analysis. Choose your method The first and most important point is that there is not…
How to analyze your Visium data
Recently we have added the 10x Genomics Visium Spatial Gene Expression solution to our portfolio. The Visium workflow generates two types of data: an H&E or Immunofluorescence (IF) tissue image and sequencing data in FASTQ files. But what are the options once you receive your data? Here, we provide you with an overview of tools…
What is Visium?
Visium Spatial Gene Expression is a spatial transcriptomics solution by 10x Genomics. In a previous blog post, we explain more about spatial transcriptomics in general, which you can read here. Here, we’ll provide you with a quick overview of the Visium Spatial Gene Expression solution, which we recently started offering as a service. A spatial transcriptomics solution Since Visium Spatial Gene Expression is a…