A5013640406- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- Biosensors and Analytical Detection
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Neuroinflammation and Neurodegeneration Mechanisms
- Gene Regulatory Network Analysis
- Memory and Neural Mechanisms
- Tryptophan and brain disorders
- Pluripotent Stem Cells Research
- Neuroscience and Neuropharmacology Research
- Genetic Associations and Epidemiology
- Immune cells in cancer
- Neurogenesis and neuroplasticity mechanisms
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Identification and Quantification in Food
- Genetics, Bioinformatics, and Biomedical Research
- Alzheimer's disease research and treatments
- Adipose Tissue and Metabolism
- Genomics and Rare Diseases
University of California, Irvine
2021-2024
Bioscience (China)
2024
Scripps Research Institute
2014
The majority of mammalian genes encode multiple transcript isoforms that result from differential promoter use, changes in exonic splicing, and alternative 3' end choice. Detecting quantifying across tissues, cell types, species has been extremely challenging because transcripts are much longer than the short reads normally used for RNA-seq. By contrast, long-read RNA-seq (LR-RNA-seq) gives complete structure most transcripts. We sequenced 264 LR-RNA-seq PacBio libraries totaling over 1...
Abstract The rise in throughput and quality of long-read sequencing should allow unambiguous identification full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by expense. Here we develop characterize Split-seq (LR-Split-seq), which uses combinatorial barcoding sequence single cells with long reads. Applied the C2C12 myogenic system, LR-split-seq associates isoforms cell types relative economy design flexibility. We find widespread evidence...
This protocol describes isolation of nuclei from brain tissues 10-week-old B6J and CASTJ mice, preparation a single nucleus suspension, selection for using Miltenyi Biotec’s Anti-Nucleus MicroBeads, fixation SHARE-seq part the Broad Institute protocol. We processed 8 samples at once (2 males 2 females per strain) with two technicians in parallel. takes about 3 hours start to finish. have successfully tested this mouse cortex (either left or right side) diencephalon (thalamus+hypothalamus)+pituitary.
This protocol describes the single-index PCR procedure for Parse Biosciences Evercode WT and Mega v2 kits. Each subpool is barcoded with a single Illumina index on 3' end of cDNA library. acts as fourth "round" cell barcoding must be included in final ID/barcode order to ensure unique barcodes across subpools within an experiment. The numerical ID sequence barcode used each are recorded experiment metadata downstream demultiplexing after sequencing run.
Mapping the impact of genomic variation on gene expression facilitates an understanding molecular basis complex phenotypic traits and disease predisposition. Mouse models provide a controlled reproducible framework for capturing breadth observed in different genotypes across wide variety tissues. As part IGVF consortium′s effort to catalog effects genetic variation, we uniformly characterized transcriptomes eight tissues from each mouse founder strain used derive Collaborative Cross strains,...
RNA abundance quantification has become routine and affordable thanks to high-throughput “short-read” technologies that provide accurate molecule counts at the gene level. Similarly of definitive fulllength, transcript isoforms remained a stubborn challenge, despite its obvious biological significance across wide range problems. “Long-read” sequencing platforms now produce data-types can, in principle, drive isoform quantification. However some particulars contemporary long-read datatypes,...
The gene expression profiles of distinct cell types reflect complex genomic interactions among multiple simultaneous biological processes within each that can be altered by disease progression as well genetic background. identification these active cellular programs is an open challenge in the analysis single-cell RNA-seq data. Latent Dirichlet Allocation (LDA) a generative method used to identify recurring patterns counts data, commonly referred topics interpret state cell. However, LDA's...
Summary Gene regulatory networks (GRNs) provide a powerful framework for studying cellular differentiation. However, it is less clear how GRNs encode responses to everyday microenvironmental cues. Macrophages can be polarized and potentially repolarized based on environmental signaling. In order identify the that drive macrophage polarization heterogeneous single-cell subpopulations are present in process, we used high-resolution time course of bulk RNA-seq ATAC-seq assays HL-60-derived...
ABSTRACT Multiple mouse models have been generated that strive to recapitulate human Alzheimer’s disease (AD) pathological features investigate mechanisms and potential treatments. The 3xTg-AD presents the two major hallmarks of AD, which are plaques tangles increase during aging. While behavioral changes accumulation well described in mice, subpopulations neurons glial cells present throughout progression not characterized. Here, we used single-cell RNA-seq microglia, single-nucleus explore...
Postnatal genomic regulation significantly influences tissue and organ maturation but is under-studied relative to existing catalogs of adult tissues or prenatal development in mouse. The ENCODE4 consortium generated the first comprehensive single-nucleus resource postnatal regulatory events across a diverse set mouse tissues. collection spans seven time points, mirroring human from childhood adulthood, encompasses five core We identified 30 cell types, further subdivided into 69 subtypes...
This protocol describes the dual-index PCR procedure for Parse Biosciences Evercode WT and Mega v2 kits. Each subpool is barcoded with two Illumina indices on 5' 3' ends of cDNA library. These acts as fourth "round" cell barcoding must be included in final ID/barcode order to ensure unique barcodes across subpools within an experiment. The numerical ID sequence barcode used each are recorded experiment metadata downstream demultiplexing after sequencing run.
This protocol describes the single-index PCR procedure for Parse Biosciences Evercode WT and Mega v2 kits. Each subpool is barcoded with a single Illumina index on 3' end of cDNA library. acts as fourth "round" cell barcoding must be included in final ID/barcode order to ensure unique barcodes across subpools within an experiment. The numerical ID sequence barcode used each are recorded experiment metadata downstream demultiplexing after sequencing run.
This protocol is an updated version of the SHARE-seq as originally described by Ma et al. in Cell (2020): https://www.sciencedirect.com/science/article/pii/S0092867420312538. The used Epigenomics Platform and Gene Regulation Observatory at Broad Institute service data production for IGVF project. slightly modified from Amelia Hall's Protocols.io protocol: https://www.protocols.io/view/share-seq-protocol-v2-2-81wgbx1oylpk/v4 with equipment personnel Mortazavi lab UCI mind. Some wording edited...
Abstract Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging study with standard short-read RNA-seq because of the uncertainties leaves about full-length structure precise termini transcripts. The rise throughput quality long-read sequencing now makes possible, principle, unambiguously identify most transcript from...
This protocol is designed for fixing single cell or nucleus suspensions the Parse Biosciences Evercode WT / Mega snRNA-seq, "Split-seq".
This protocol describes the original Parse Biosciences Evercode WT v2 for single-nucleus or single-cell RNA-seq of 100,000 nominal nuclei cells. Unlike other scRNA-seq methods that physically separate individual cells into different compartments to label transcripts with cell-specific barcodes, uses (or nuclei) themselves as “containers” in which intracellular are labeled using combinatorial indexing. In practice, split wells, a well-specific barcode is appended transcripts, and then pooled...
This protocol describes the original Parse Biosciences Evercode WT Mega v2 for single-nucleus or single-cell RNA-seq of 1,000,000 nominal nuclei cells. Unlike other scRNA-seq methods that physically separate individual cells into different compartments to label transcripts with cell-specific barcodes, uses (or nuclei) themselves as “containers” in which intracellular are labeled using combinatorial indexing. In practice, split wells, a well-specific barcode is appended transcripts, and then...
This protocol describes a modified version of the Parse Biosciences Gene Capture for full-length cDNA meant both Illumina short read and Oxford Nanopore long library prep sequencing. We use Twist exome panels to enrich non-intronic reads more meaningful long-read data. Each section matches original but with our modifications. Please see attachment protocol. The main deviations from are 1. amplification reagents instead included in kit, 2. modification SPRI bead ratio 1.8x 0.8x. perform this...