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 […]
tSNE
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
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
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 […]
scRNA-sequencing data quality control
Quality control is the basic step in any single-cell sequencing data analysis. This comes in two parts. First, performing quality control on cells by removing outliers, any doublet or dead cells that we don’t want to include in the analysis. The second is doing quality control on genes which means focusing on certain sets of […]
Inspiring the next generation of scientists – a new blog post from STACCATO ESR is live
This March our ESR4 James Clubb gave a scientific workshop to a group of five to seven year old students at an international kindergarten in Helsinki, Finland. In a new STACCATO ESR blog post, James shares insights from his experience and looks back on an exciting day with a ”new generation of scientists”. Are you […]
3rd place in the Langen Junior Science Award
On 08 April 2022, Filippos Theofilos Charitidis (ESR9) received 3rd place in the Langen Junior Science Award for his publication on “Monitoring CAR T cell generation with a CD8-targeted lentiviral vector by single-cell transcriptomics”. The Langen Junior Science Award is awarded annually in recognition of particularly significant publications by young scientists of the Paul Ehrlich […]
STACCATO has its YouTube channel
“Video is the next wave, and scientists must be prepared for it,” says McKee in her know-how for scientists, The Scientist Videographer. YouTube is a particularly relevant platform because of its enormous reach: it is the second most accessed website worldwide (Alexa, 2020), where 2 billion registered users watch videos monthly. Recognizing the potential that […]
