Publications by Riccardo Dainese

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Bart Deplancke, Daniel Migliozzi, Riccardo Dainese, Daniel Alpern, Gilles Weder, Mustafa Demir, Dariia Gudkova, Hüseyin Baris Atakan

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Springer2024

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Daniel Alpern

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve e ...

2023

Biological material pooling device for biological or biomolecule purification

Bart Deplancke, Riccardo Dainese, Daniel Alpern

The present invention concerns a biological material pooling device for biological or biomolecule purification comprising a receptacle including a first orifice comprising ordefining a rectangular opening, the receptacle being configured to receive at leas ...

2023

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Bart Deplancke, Riccardo Dainese, Daniel Alpern, Mustafa Demir

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said meth ...

2022

Deterministic scRNA-seq captures variation in intestinal crypt and organoid composition

Matthias Lütolf, Bart Deplancke, Esther Amstad, Vincent Roland Julien Gardeux, Julie Marie Russeil, Rita Sarkis, Jörn Pezoldt, Johannes Julius Bues, Antonius Chrisnandy, Riccardo Dainese

DisCo is a deterministic droplet microfluidics tool for single-cell analysis on low cell input samples, which is demonstrated to profile individual intestinal organoids and in vivo-derived small tissues. ...

NATURE PORTFOLIO2022

Live-seq enables temporal transcriptomic recording of single cells

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Orane Josiane Guillaume-Gentil, Wanze Chen, Pernille Yde Rainer, Magda Zachara, Wouter Saelens

Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize cellular heterogeneity(1). However, scRNA-seq requires lysing cells, which impedes further molecular or functional analyses on the same cells. Here, we established Liv ...

NATURE PORTFOLIO2022

A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation

Freddy Radtke, Bart Deplancke, Ute Koch, Vincent Roland Julien Gardeux, Julie Marie Russeil, Jörn Pezoldt, Judith Franziska Kribelbauer, Riccardo Dainese, Daniel Alpern, Maria Litovchenko

Non-coding variants coordinate transcription factor (TF) binding and chromatin mark enrichment changes over regions spanning >100 kb. These molecularly coordinated regions are named "variable chromatin modules" (VCMs), providing a conceptual framework of h ...

Nature Portfolio2022

cis-regulatory variation modulates susceptibility to enteric infection in the Drosophila genetic reference panel

Bart Deplancke, Vincent Roland Julien Gardeux, Maroun Bou Sleiman, Virginie Sandra Braman, Riccardo Dainese, Maria Litovchenko, Michael Vincent Frochaux, Dani Osman, Brian Dennis Hollis, Tommaso Andreani

Background: Resistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understan ...

2020

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Bart Deplancke, Vincent Roland Julien Gardeux, Riccardo Dainese, Jia Yuan Jiang, Daniel Alpern, Antonio Carlos Alves Meireles Filho, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molec ...

National Academy of Sciences2020

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo

Riccardo Dainese

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

EPFL2019