The STACCATO PhD Students Podcast gets a visit from Becton Dickinson Research Centre Ireland
The latest episode of the STACCATO PhD Students Podcast is here and gets a special visit from Padraig Fitzgerald, Senior R&D Director from Becton Dickinson Research Centre Ireland (BD). In a conversation with our early-stage researcher Teresa (ESR1), Padraig Fitzgerald provides an exciting introduction to the work of BD and explains why they have become […]
The STACCATO PhD Students Podcast goes into the next round!
This week, our STACCATO PhD Student Podcast offers another unique insight into life as a STACCATO early-stage researcher. This week, our two ESRs Filip (ESR9) and Elham (ESR10), talk to Naphang and Alex, two PhD fellows in an exciting multidisciplinary plenary about their projects and experiences. The conversation around CAR-T cells provides unique and interesting […]
New episode of the STACCATO PhD Students Podcast!
The STACCATO Podcast is slowly but surely kicking into gear. Every week, STACCATO PhD students provide exciting insights into their research as they share their experiences of working on the STACCATO project. This week our ESR2 Alan explains his ESR project in a light and conversational way, quickly engaging a wide audience on topics such […]
The brand new STACCATO PhD Students Podcast is here!
The new STACCATO Podcast is here. In this new format, our talented PhD students will talk about their experiences and research on cells to develop new manufacturing methods for biopharmaceuticals. Every week, STACCATO PhD students provide exciting insights into their research as they share their experiences of working on the STACCATO project. In a first […]
Life as a PhD Student – a new blog post is live
Teresa Swift joined the STACCATO Training Network in 2019 as an Early Stage Researcher working towards her PhD in single cell multi-omics. Approaching the end of her STACCATO project, she takes a look back at her experiences and talks about her life as a PhD student in our latest blog post. Teresa shares her impressions […]
Theofilor Filippos Chartidis (ESR9): Elevator Video Pitch
Theofilor Filippos Chartidis (ESR9) is conducting research on CAR-T cells at the Paul Ehrlich Institute as part of his STACCATO ESR Research Project. CAR-T cells are immune system cells (T cells) of cancer patients, which are equipped with a chimeric antigen receptor (CAR) outside the body by means of gene transfer. With the help of […]
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 […]
UMAP
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 […]
