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Primeur weekly 2018-06-11

Focus

Exchange of experience and focus on specialisation are key to Europe regaining status in EuroHPC and e-Infrastructures ...

Quantum computing

Atos Quantum Learning Machine available at SURFsara ...

Silicon provides means to control quantum bits for faster algorithms ...

Designer materials with completely random structures might enable quantum computing ...

Rutgers-led research could lead to more efficient electronics ...

Focus on Europe

Researchers at CNAG-CRG developed a novel computational tool named BigSCale to analyze millions of single cells simultaneously ...

Pawsey and PRACE to jointly promote the use of supercomputing ...

Bright and BeeGFS share plans for TERATEC 2018 Forum ...

GCS supports three German university teams in 2018 ISC Student Cluster Competition ...

Hardware

Dell EMC PowerEdge servers enable University of Sydney's world-leading artificial intelligence research ...

Comino announces Comino Grando, a liquid-cooled supercomputer set to disrupt cryptocurrency mining and solve its energy crisis ...

National Science Foundation supports development of new nationwide data storage network ...

Pushing boundaries for CPUs and GPUs, AMD shows next-generation of Ryzen, Radeon and EPYC product leadership at Computex 2018 ...

GARR powers National Research and Education Network in Italy with Infinera Cloud Xpress 2 ...

Supermicro brings resource saving green computing to Computex Taipei 2018 ...

Applications

Cray partners with Digital Catapult's Machine Intelligence Garage to drive UK artificial intelligence innovation ...

Swimming in schools saves energy ...

Researchers use artificial intelligence to identify, count, and describe wild animals ...

Scientists find ordered magnetic patterns in disordered magnetic material ...

New model sheds light on key physics of magnetic islands that halt fusion reactions ...

TOP500

Oak Ridge National Laboratory launches Summit supercomputer ...

Researchers at CNAG-CRG developed a novel computational tool named BigSCale to analyze millions of single cells simultaneously

6 Jun 2018 Barcelona - New research led by Holger Heyn at the CNAG-CRG, presents a sophisticated computational framework to analyze single-cell gene expression levels, scalable to process millions of individual cells. The work, published in the current issue of the scientific journalGenome Research, shows for the first time a tool capable of analyzing such large single-cell RNAseq dataset. This dramatically extends the limits of single-cell genome research.

All the cells in a human body share the same genome but each cell has the potential to become specific in a tissue or organ due to gene expression. Scientists worldwide are looking at what differentiates one cell from another. One of the current challenges of genome research is to analyze many individual cells in order to find and to identify those differences. The analysis of individual cell using single-cell RNA sequencing has been crucial to face this challenge and revolutionized our understanding of the complexity of tissues, organs and organisms. Looking at gene expression of one cell at a time, scientists are now able to describe a sample's heterogeneity at unprecedented resolution and without prior knowledge of its composition.

Accordingly, large-scale single-cell projects led to the identification of previously unknown cell types and to the drawing of comprehensive cellular maps of organisms. Within the framework of the Human Cell Atlas project, researchers aim at creating an atlas of all cell types that make up a human body. However, such studies create massive amounts of sequencing data and analyzing large datasets are a major challenge.

A group of scientists of the CNAG-CRG, in collaboration with researchers from the University Pompeu Fabra (UPF) and the Spanish Biomedical Research Consortium on Rare Diseases (CIBERER), has now developed an efficient computational framework that enabled processing, analysis and interpretation of such big-scale single-cell experiments. The group illustrated the power of their strategy by analyzing one of the largest single-cell studies with 1.3 million individual cells of the developing mouse brain.

"BigSCale is extremely powerful in identifying cell type specific genes, which greatly helps in the downstream interpretation of experiments", stated Holger Heyn, CNAG-CRG's Single Cell Genomics team leader and senior author of the study. The novelty of the analytic tool named "BigSCale" lies in a numerical model that sensitively determines differences between single cells. Having charted how individual cells differ from each other, they can be grouped together into populations of cells to describe the cellular complexity of a given tissue. As virtually all tissues are composed of different cell types and subtypes, such an analysis can guide an unbiased in-depth characterization without initial hypotheses. Differentially expressed marker genes between subpopulation help the researcher to link cells to prior knowledge about the tissue anatomy or to describe the functions of newly discovered cell types.

In addition, the tool was designed to tackle future challenges of large datasets. "The costs to derive single-cell profiles are decreasing and we are seeing studies of increasing cell numbers", added Dr. Heyn. In this regard, a module in the BigSCale workflow enables the analysis of millions of cells through a directed convolution strategy. Here, single-cell transcriptomes from similar cells are merged into index cells, which greatly reduces the amount of data to be processed.

With the new tool in hand the group analyzed one of the largest single-cell gene expression dataset of 1.3 million cells, a resource publically available from 10x Genomics. "BigSCale allowed us to look deep into the developmental processes of the mouse brain and to characterize even rare neuronal cell types", commented Giovanni Iacono, the first author of the work. Specifically, the high number of cells enabled the group to zoom into a small transient cell population called Cajal-Retzius cells and to describe major substructures related to distinct differentiation stages, spatial organisation and cellular function. "The BigSCale framework provides a powerful solution for virtually any species and is even applicable outside the RNA sequencing context", explained Dr. Heyn and added: "We expect it to contribute to the interpretation of large-scale studies, such as the Human Cell Atlas project."

This work received funding and has been supported by the Fundación Ramón Areces, the marathon "Todos somos raros, todos somos únicos", the EU Marie Curie Fellowships, the Instituto de Salud Carlos III, Spanish Ministry of Economy, Industry and Competitiveness, the Catalan Government, and the European Regional Development Fund (ERDF).

The paper titled " bigSCale: an analytical framework for big-scale single-cell data " has been published inGenome Research.
Source: Centre Nacional d'Analisi Genomica - Centre for Genomic Regulation - CNAG-CRG

Back to Table of contents

Primeur weekly 2018-06-11

Focus

Exchange of experience and focus on specialisation are key to Europe regaining status in EuroHPC and e-Infrastructures ...

Quantum computing

Atos Quantum Learning Machine available at SURFsara ...

Silicon provides means to control quantum bits for faster algorithms ...

Designer materials with completely random structures might enable quantum computing ...

Rutgers-led research could lead to more efficient electronics ...

Focus on Europe

Researchers at CNAG-CRG developed a novel computational tool named BigSCale to analyze millions of single cells simultaneously ...

Pawsey and PRACE to jointly promote the use of supercomputing ...

Bright and BeeGFS share plans for TERATEC 2018 Forum ...

GCS supports three German university teams in 2018 ISC Student Cluster Competition ...

Hardware

Dell EMC PowerEdge servers enable University of Sydney's world-leading artificial intelligence research ...

Comino announces Comino Grando, a liquid-cooled supercomputer set to disrupt cryptocurrency mining and solve its energy crisis ...

National Science Foundation supports development of new nationwide data storage network ...

Pushing boundaries for CPUs and GPUs, AMD shows next-generation of Ryzen, Radeon and EPYC product leadership at Computex 2018 ...

GARR powers National Research and Education Network in Italy with Infinera Cloud Xpress 2 ...

Supermicro brings resource saving green computing to Computex Taipei 2018 ...

Applications

Cray partners with Digital Catapult's Machine Intelligence Garage to drive UK artificial intelligence innovation ...

Swimming in schools saves energy ...

Researchers use artificial intelligence to identify, count, and describe wild animals ...

Scientists find ordered magnetic patterns in disordered magnetic material ...

New model sheds light on key physics of magnetic islands that halt fusion reactions ...

TOP500

Oak Ridge National Laboratory launches Summit supercomputer ...