Identifying differentially expressed genes by scRNA-seq

Single-cell RNA sequencing (scRNA-seq) comprises a state-of-the-art technology for analysing the gene expression profile of individual cells from a complex or even a uniform specimen. Differential gene expression analysis and Uniform Manifold Approximation and Projection (UMAP) plots may reveal transcriptomic differences among cell populations, pointing out genes that are either upregulated or downregulated in relation […]


Uniform Manifold Approximation and Projection (UMAP) is a dimensionality reduction technique to construct graphs showing the complexity of specimens and how the cell clusters diverse between each other according to a selected group of features (i.e. genes). Principal component analysis (PCA) prior UMAP plotting speeds up the computational process. It is closely related with t-distributed […]

Next generation sequencing basics – RNA

RNA-sequencing (RNA-seq) is a technique that utilises next-generation sequencing to investigate gene expression in cells by quantifying the presence and amount of RNA reads within a sample. This allows scientist to explore the cellular transcriptome (total cellular RNA content including mRNA, ncRNA, miRNA, etc.), evaluate changes in gene expression (e.g. caused by changes in environmental […]

Experimental design for single cell analysis

It is challenging to create generalizable designs for single-cell transcriptomic experiments because each one requires the user to make informed decisions in order to obtain interpretable results. These include the selection of sample types, cell numbers and preparation methods; the choice of scRNA-seq techniques and sequencing parameters; and the design of computational analysis strategies to […]

Integrating scRNA-seq and scATAC-seq data

Single cell RNA sequencing (scRNA-seq) has exemplified recent advances in the anlaysis of transcriptomic heterogeneity, enabling the characterisation of gene expression in individual cells. The utility of scRNA-seq data can be further enhanced through combination with other technologies that have been developed to capture other molecular measurements. For example, single cell assay for transposase-accessible chromatin […]


t-distributed stochastic neighbor embedding or more commonly referred to as tSNE is technique used to reduce the dimensions of a data set, but why is this desired? Effective data visualization can only be done in a couple dimensions, so when there are many variables, such is the case in single cell transcriptomics, reducing the number […]


Perfusion is a type of cultivation method for cells. It is very similar in operation to a continuous stirred tank except that there is a device on the outflow that retains the cells and returns them back to the reactor. This type of cultivation can be used with mammalian cells to achieve high cell densities. […]


Mitochondria are the powerhouse of the cell. Distinctively, they contain their own DNA termed Mitochondrial DNA (mtDNA). Each mammalian cell contains thousands of copies of mtDNA. When all copies within a cell are identical, the cell exists in a state known as “homoplasmy”. Sometimes, a mutation might occur in a copy of mtDNA. Because there […]

FN-Silk (Biosilk)

FN-Silk is a self-assembling spider silk functionalized with a Fibronectin to promote cell adhesion used for advanced 3D cell culture. It has been shown to be non-immunogenic and biodegradable. Cells are highly proliferative within FN-silk promoted by an efficient diffusion of oxygen and nutrients. builts up different structures such as membranes, foam networks and fibers […]

Single cell transcriptomics – a gerneric explanation of common steps

Single-cell RNA sequencing (scRNA-seq) has significantly advanced our knowledge of biological systems by studying the single cell transcriptome. Compared to bulk RNA-seq, scRNA-seq is able to study cellular heterogeneity. BDTM Rhapsody Steps of single cell transcriptomics Capture single cells Magnetic barcoded beads to microwells (one bead to one cell) Cell lysis to hybridize mRNA´s onto […]