A human liver model leads to therapeutic discovery for liver disease

In this blog, we will discuss how single-cell RNA sequencing contributed to the discovery of a therapeutic for the treatment of advanced liver disease.   Liver fibrosis can lead to cirrhosis, which is a late-stage liver disease in which a large part of the liver tissue is replaced by fibrotic tissue, and to hepatocellular carcinoma (HCC)….

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Transcriptome of human FDCs reveals role in antigen presentation to B cells and regulation of T cells 

In this blog, we will discuss the contribution of single-cell RNA sequencing to uncovering the function of human follicular dendritic cells (FDCs) in the germinal center (GC) microenvironment.    The GC is a structure in secondary lymphoid tissues, such as tonsils, in which long-lived antibody-secreting plasma cells and memory B cells are produced. Within the GC,…

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How to get started with your own data analysis

There is not one generally accepted and failsafe way to analyze single-cell data. With data analysis, there are many different methods or software solutions. A general way forward is to briefly test several of them in an exploratory effort to find one that works best for your data and biological question. Broadly speaking, there are…

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Materials & Methods

Acknowledgements Please mention Single Cell Discoveries in your acknowledgements if we helped you with single-cell sequencing experiments and/or data analysis. We always love to know when our clients have published data generated by our services, so please also let us know if your paper will come online, so we can help promote it. Sample text…

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What is VASA-seq?

VASA-seq is based on 384-well cell capture plates and flow cytometry (FACS) sorting. However, unlike other single-cell sequencing technologies, it does not rely on primers that bind to the endogenous poly-A tail of mRNA molecules. This means that the technique allows us to analyze non-coding RNA species and immature mRNA molecules simultaneously, all at single-cell…

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What is Bulk RNA sequencing?

Bulk RNA-sequencing is the method of choice for transcriptomics analysis of pooled cell populations, tissue sections, or biopsies. It measures the average expression level of individual genes across hundreds to millions of input cells and is useful to get a global idea of differences in gene expression between samples.At Single Cell Discoveries, we can offer…

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What is 10x Genomics?

10x Genomics is a microfluidics-based method of single-cell RNA sequencing. The technique makes use of the Chromium system, a device that enables single-cell sequencing with their Next GEM technology. The biology behind 10x Genomics  10x Genomics offers multiple products that can be used on the chromium controller, each with their own applications. Currently, we offer…

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What is SORT-seq?

SORT-seq is a plate-based method of single-cell RNA sequencing. The technique makes use of 384-well microplates, called cell-capture plates, containing well-specific barcoded primers. SORT-seq (Muraro et al. 2016) is a partially robotized version of the CEL-seq2 protocol (Hashimshony et al. 2016). Cell-capture plates Cell capture plates offer a flexible platform for single-cell sequencing. Single cells…

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QC

QC | SORT-seq Bioanalyzer plots  During the processing of SORT-seq plates, we check the amount of aRNA and cDNA and the quality of the samples. The plot it generates is a QC metric to study the concentration and size distribution of library fragments and is the first indication of the quality of the sample.   The QC results depend e.g. on the cell type that was sorted (some cells have more…

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Transcription factors EOMES and T-BET regulate maturation of NK cells 

In this blog, we will discuss how two transcription factors influence the maturation of natural killer (NK) cells.   NK cells are cells of the innate immune system and are part of the group 1 innate lymphoid cells (ILCs). NK cells are important for antiviral and antitumor responses. Before NK cells are fully functionally active, they…

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The influence of lipid droplets on brain stem cells 

In this blog, we will discuss how lipid droplets can influence the stem cells in the brain. Stem cells are undifferentiated cells that can develop in different types of cells. In the brain, neural stem/progenitor cells (NSPCs) have the potential to develop into neurons and other brain cells. Lipid metabolism influences the activity of NSPCs….

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