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

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, Riccardo Dainese, Daniel Alpern, Vincent Roland Julien Gardeux

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, Mustafa Demir, Riccardo Dainese, Daniel Alpern

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, Saba Rezakhani, Esther Amstad, Riccardo Dainese, Julie Marie Russeil, Antonius Chrisnandy, Vincent Roland Julien Gardeux, Johannes Julius Bues, Marjan Biocanin, Rita Sarkis, Jörn Pezoldt

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

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

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

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

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

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

A Comprehensive Drosophila melanogaster Transcription Factor Interactome

Jean-Daniel Feuz, Bart Deplancke, Riccardo Dainese, Sachi Iiyama Inukai

Combinatorial interactions among transcription factors (TFs) play essential roles in generating gene expression specificity and diversity in metazoans. Using yeast 2-hybrid (Y2H) assays on nearly all sequence-specific Drosophila TFs, we identified 1,983 pr ...

2019

ZFP30 promotes adipogenesis through the KAP1-mediated activation of a retrotransposon-derived Pparg2 enhancer

Carine Delattre-Gubelmann, Didier Trono, Julien Léonard Duc, Bart Deplancke, Sunil Kumar Raghav, Marco Cassano, Michaël Imbeault, Petra Catalina Schwalie, Suk Min Jang, Riccardo Dainese, Julie Marie Russeil, Wanze Chen, Evgeniia Pankevich

Krüppel-associated box zinc finger proteins (KZFPs) constitute the largest family of mammalian transcription factors, but most remain completely uncharacterized. While initially proposed to primarily repress transposable elements, recent reports have revea ...

Nature Research2019

System for capture or immunoprecipitation of a protein-dna complex

Bart Deplancke, Riccardo Dainese

The present invention concerns a system for immunoprecipitation of a protein-DNA complex or for capture of a protein-DNA complex including: - a microfluidic device including a plurality of antibody units, wherein each antibody unit includes at least one mi ...

2019

Adaptive damage retention mechanism enables healthier yeast population

Riccardo Dainese

During cytokinesis in budding yeast (Saccharomyces cerevisiae) damaged proteins are distributed asymmetrically between the daughter and the mother cell. Retention of damaged proteins is a crucial mechanism ensuring a healthy daughter cell with full replica ...

ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD2019

Simplified Drop-seq workflow with minimized bead loss using a bead capture and processing microfluidic chip

Bart Deplancke, Esther Amstad, Riccardo Dainese, Johannes Julius Bues, Marjan Biocanin

Single-cell RNA-sequencing (scRNA-seq) has revolutionized biomedical research by enabling the in-depth analysis of cell-to-cell heterogeneity of tissues with unprecedented resolution. One of the catalyzing technologies is single cell droplet microfluidics, ...

2019

Device for high throughput single-cell studies

Bart Deplancke, Riccardo Dainese, Johannes Julius Bues, Marjan Biocanin

The present invention concerns a microfluidic device or chip including at least one inlet for introducing at least one object into the device; an oil inlet for introducing an oil that supports droplet formation into the device or a droplet forming substanc ...

2018

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Philipp Bucher, Didier Trono, Giovanna Ambrosini, Bart Deplancke, Romain Fernand Pietro Groux, Alina Isakova, Pernille Yde Rainer, Michaël Imbeault, Riccardo Dainese, Daniel Alpern

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017