OUR RESEARCH TOOLS
We employ a diverse range of techniques that significantly contribute to various areas of genetic, genomic and developmental biology research.
GWAS
GWAS (Genome-Wide Association Studies) allows us to identify genetic variants associated with specific traits or diseases by comparing the genomes of large populations. This technique has been instrumental in unraveling the genetic basis of complex diseases and understanding the role of genetic variations in human health. In the Sobreira lab, we utilize GWAS as a starting point, and then employ pipelines to prioritize genes and regions of interest. These prioritized candidates are then subjected to functional analysis, allowing us to gain further insights into their roles and mechanisms in disease development and progression.
Genetic Variant
Genetic variants, particularly single nucleotide polymorphisms (SNPs), are changes in DNA that can impact gene expression. Some of the most critical genetic variants occur in regulatory regions of the genome, which control when and how genes are turned on or off. In the Sobreira lab, we conduct extensive analyses of genetic variants to unravel their potential associations with diverse phenotypic traits and diseases, providing valuable insights into the underlying genetic architecture. However, our research goes beyond mere identification and association. We delve into the functional impact of these genetic variants, aiming to deepen our understanding of their contributions to the development of complex diseases, including obesity, neurological disorders, cancer, and type 2 diabetes.
Expression data
Sobreira lab employs cutting-edge techniques for comprehensive analysis of gene expression patterns. By studying the transcriptome, we identify differentially expressed genes and unravel their critical roles in specific biological processes. This approach helps us uncover novel biomarkers and pathways associated with diseases, advancing our understanding of gene regulation in complex biological systems. We utilize bulk RNA sequencing (RNA-seq) and single-cell RNA sequencing (scRNA-seq) to explore gene expression at macro- and microscale resolutions. Bulk RNA-seq enables us to analyze gene expression patterns across entire tissue samples, identifying differentially expressed genes in different conditions or disease states. With scRNA-seq, we study gene expression profiles at the individual cell level, providing unparalleled resolution to detect rare cell populations and cellular heterogeneity.
Chromatin state
In the Sobreira lab, our research focuses on conducting comprehensive investigations into the chromatin state, which encompasses the organization and accessibility of DNA within the cell nucleus. To accomplish this, we employ advanced chromatin profiling techniques such as ChIP-seq, Cut and Run, Cut and Tag and ATAC-seq. These powerful methods allow us to gain valuable insights into the intricate chromatin landscape, enabling us to identify specific regions that play significant roles in gene regulation and essential cellular processes. By unraveling the complexities of the chromatin state, we deepen our understanding of how DNA packaging influences gene expression and contribute to a broader comprehension of cellular function and disease mechanisms.
Genome editing
In the field of genome editing, the Sobreira lab utilizes the power of CRISPR-Cas9 technology. This groundbreaking technique has revolutionized the field of genetic engineering, enabling precise modifications to specific regions of the genome. With CRISPR-Cas9, targeted gene knockout, gene insertion, or gene editing can be achieved with unprecedented accuracy and efficiency. The versatility and precision of CRISPR-Cas9 have opened up new avenues for research and hold tremendous potential for therapeutic applications. In the Sobreira lab, we leverage this transformative technology to advance our understanding of genetic mechanisms, develop innovative disease models, and pave the way for future therapeutic interventions.
3D chromatin conformation
To unravel the intricate three-dimensional organization of the genome, we employ advanced techniques such as 3D chromatin conformation analysis, including Hi-C seq and 4C-seq. These cutting-edge methodologies allow us to delve into the physical interactions between genomic regions, shedding light on the spatial organization and functional relationships between genes and regulatory elements. Our investigations into 3D chromatin conformation provide a deeper understanding of how the spatial organization of the genome influences gene expression and cellular function, paving the way for breakthroughs in the field of genomics and its implications for human diseases risk.
Reporter Assays
In the Sobreira lab, reporter assays play a pivotal role in our investigations, providing us with essential tools to explore the functional significance of genetic variations and regulatory elements. These assays enable us to investigate the activity of promoters, enhancers, and other regulatory regions by introducing specific DNA sequences into reporter constructs. Sobreira lab utilizes the powerful combination of Luciferase assays and Massively Parallel Reporter assay (MPRA) to gain comprehensive insights into the functional consequences of genetic variations and regulatory elements. These techniques serve as indispensable tools to understand the regulatory impact of genomic variation.
Tissue Culture
Through tissue culture, we gain the ability to closely observe and analyze cellular behavior, conduct experiments, and perform a wide range of assays that allow us to delve into specific biological phenomena. The Sobreira lab harnesses the tremendous potential of human induced pluripotent stem cells (iPSCs) and their remarkable ability to differentiate into various specialized cell types. By utilizing iPSCs, we can manipulate their fate and guide their differentiation into specific lineages, such as neurons, adipocytes, and cardiomyocytes. This approach offers a unique opportunity to study and compare the characteristics, functions, and responses of different cell lineages derived from various donors, shedding light on fundamental processes of cellular development, tissue regeneration, and disease pathogenesis.
Cell phenotyping
Cell phenotyping is another essential technique we utilize, which involves characterizing and classifying cells based on their specific properties and markers. Through cell phenotyping, we gain insights into cell types, cell states, and cellular heterogeneity, contributing to a comprehensive understanding of complex biological systems. This information helps us unravel the intricacies of cell function, development, and disease progression.
Cell imaging
Cell imaging is a powerful tool we employ to visualize cellular structures, processes, and interactions. By using advanced microscopy techniques, we can capture high-resolution images of cells and their components, enabling us to analyze their morphology, subcellular localization, and dynamic behavior. Cell imaging allows us to observe cellular processes in real-time and provides valuable visual evidence to support our research findings.
Fine Mapping
Fine mapping is a technique we utilize to narrow down the genomic regions associated with specific traits or diseases. By analyzing genetic variants and their relationships with phenotypic outcomes, we can identify regions of interest within the genome that may be involved in disease susceptibility or important biological functions. Fine mapping helps us refine our understanding of the genetic architecture underlying complex traits, paving the way for targeted investigations and potential therapeutic interventions.
eQTL
eQTL analysis, or expression quantitative trait loci analysis, is a technique we employ to explore the relationship between genetic variants and gene expression levels. By studying the association between genetic variations and gene expression patterns, we gain insights into how genetic differences influence the regulation of gene expression. This technique helps us uncover potential causal links between genetic variants and specific phenotypic traits or diseases, contributing to our understanding of the molecular mechanisms underlying complex traits.
Clinic
The Sobreira Lab has established fruitful collaborations with physicians to bridge the gap between scientific research and clinical practice. By partnering with physicians, the lab aims to enhance the understanding of diseases, develop innovative diagnostic tools, and improve patient care. Through this collaboration, the Sobreira Lab leverages the expertise and clinical insights of physicians, while providing valuable scientific knowledge and research findings to inform medical decision-making and advance medical treatments. Together, the Sobreira Lab and physicians work synergistically to drive scientific discoveries from the laboratory bench to the patient's bedside, ultimately contributing to improved healthcare outcomes.
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