Project description:We developed HyDrop, a new droplet microfluidic single-cell sequencing protocol for single-cell ATAC-seq and single-cell RNA-seq. We applied HyDrop-ATAC to flash-frozen mouse cortex and generated 7996 single-cell chromatin accessibility profiles. We applied HyDrop-RNA to flash-frozen mouse cortex and generated 9508 single-cell transcriptomes. We also applied HyDrop-RNA to a small population of FAC-sorted neurons from the Drosophila brain to demonstrate the protocol's applicability to low-input samples. The data available in this repository can be used to replicate all the figures in our manuscript using our data analysis tutorial available here: https://github.com/aertslab/hydrop_data_analysis
Project description:DNA barcodes can be used to identify single cells in a sequencing data space while optical codes can be used to track single live cells in an image data space. We have developed dual image and DNA (ID)-coding, which identifies individual single cells in both live image and sequencing data spaces. Samples provided here are relevant to proof-of-concept studies of ID-coding presented in the associated publication. DNA barcoded micro-particles were encapsulated in hydrogel droplets with or without single cells. The hydrogel droplets were then subjected to “single-droplet sequencing” where whole polyA-bearing nucleic acid components within a hydrogel droplet (i.e. mRNA from cells and synthetic DNA on beads) were concatenated by the same cell barcodes.
Project description:Plasmodium-specific CD4+ T cells from mice infected with Plasmodium chabaudi chabaudi AS parasites were recovered at Days 0, 4, 7, and 32 to undergo processing and to generate scATAC-seq dataset. At Day 7, CXCR5+ and CXCR6+ cells were recovered separately. At Day 32, mice were administered with either saline or artesunate (intermittent artesunate therapy - IAT). scATAC-seq dataset was analysed to investigate epigenomic landscapes of CD4+ T cells from effector to memory states.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.
Project description:To study developmental trajectories in brain organoids, we conducted scRNA-seq and scATAC-seq in parallel on a dense timecourse of early development.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.
Project description:Progress in sample preparation for scRNA-seq is reported based on RevGel-seq, a reversible-hydrogel technology. Barcode bead-cell tandems stabilized by a chemical linker are dispersed in the hydrogel in the liquid state. Upon gelation the tandems are immobilized, cell lysis is triggered by detergent diffusion, and RNA molecules are captured on the adjacent barcode beads. After reverse transcription and preparation for cDNA sequencing, bioinformatic analysis reveals performance quality comparable to microfluidic-based technologies.