What is Microarray?

A microarray is a laboratory tool used to detect the expression of thousands of genes simultaneously. It consists of a small solid support, usually a glass slide, onto which DNA molecules are fixed in an orderly manner. These DNA molecules, also known as probes, are used to hybridize cDNA or cRNA from samples. By measuring the hybridization patterns, researchers can determine the expression levels of various genes, providing insights into gene activity under different conditions. This technology is widely used in genomics, enabling the analysis of gene expression, gene mutations, and genetic variations across large numbers of genes.

Importance of Microarray in Life Science R&D

Microarray technology has revolutionized research and development in life sciences. Its importance can be highlighted in several key areas:

1. Gene Expression Profiling: Microarrays allow scientists to monitor the expression levels of thousands of genes at once, providing comprehensive data on gene activity in different tissues, stages of development, or in response to treatments.
2. Disease Research: By comparing gene expression profiles between healthy and diseased tissues, researchers can identify genes involved in diseases such as cancer, diabetes, and neurological disorders, leading to better understanding and potential therapeutic targets.
3. Drug Development: Pharmaceutical companies use microarrays to identify the effects of drugs on gene expression, which aids in the discovery of new drugs and the optimization of existing ones.
4. Genetic Mapping: Microarrays facilitate the detection of single nucleotide polymorphisms (SNPs) and other genetic variations, contributing to the mapping of genomes and the study of genetic predispositions to diseases.

Harmonized Microarray Data

The vast amount of data generated by microarray experiments requires careful management and harmonization to ensure its usability and reproducibility. Harmonized microarray data involves the standardization of data formats, normalization of expression levels, and the integration of data from multiple sources. This standardization enables researchers to compare data across studies thereby increasing the robustness and reliability of their findings. Harmonized data can be reused in meta-analyses, enabling broader insights and new discoveries without the need for new experiments. It can also be easily shared within the scientific community, fostering collaboration and accelerating the pace of research.

Elucidata's Solutions and Services for Harmonized Microarray Data

Elucidata offers cutting-edge solutions and services to help researchers harness the full potential of microarray data. Our platform and services include:

1. Data Harmonization: All microarray datasets on Elucidata's data harmonization platform, Polly, will have  Log₂(X+1) transformed count values (unless transformed counts are available at source). Polly ensures data precision with no feature loss, including all sample and feature metadata from in-house and public sources. Elucidata’s team of experts process data using custom pipelines as required and provide data in the necessary format tailored for your research needs (not necessarily log-transformed). Our experts conducts meticulous QA/QC checks, guaranteeing metadata completeness and schema compliance. We eliminate technical artifacts and redundancies, ensuring your data is analysis-ready. Transparency is key: you (user) can review the annotation methods and QC metrics applied to your microarray datasets by accessing detailed QA/QC reports directly from your Atlas on Polly.
2. Custom Curation: Polly allows customization of metadata curation, cohort creation, and cohort comparisons to meet specific analysis needs.  By transforming complex probe IDs into meaningful gene symbols, Polly enables feature-level queries and simplifies analysis for deeper insights. You can visualize enriched genes and pathways through interactive volcano plots, heat maps, and other tools. Additionally, you can convert selected in-house or public datasets into RDS objects using pre-configured Polly notebooks, allowing seamless integration into your internal analysis pipelines.
3. Ontology Backed Sample-level Metadata: Polly employs standardized vocabularies and ontologies, such as MeSH, BRENDA Tissue Ontology, NCBI Taxonomy, and Cell Ontology or any pre-defined  vocabularies based on users' requirements to consistently annotate critical metadata fields like disease, tissue, organism, and cell type. Elucidata employs a human-in-the-loop AI approach to enhance metadata annotation, combining automated tools with expert human curation. This system ensures high-quality metadata assignments by leveraging AI algorithms to standardize and suggest appropriate ontology terms. Human experts validate and refine these annotations, especially in complex or ambiguous cases.
4. Data Management: Polly streamlines data management by automatically ingesting microarray data from various sources such as ELN, S3 buckets, and CROs, eliminating the need for manual data entry. It cleans, harmonizes, and structures datasets according to your custom schema, allowing you to focus on discovery rather than data wrangling. By integrating multi-modal datasets into a central Atlas, Polly helps unveil hidden patterns and accelerate research breakthroughs. Additionally, Polly enables effortless management and analysis of terabytes of both in-house and publicly available microarray data on a secure cloud platform.

Know More

By leveraging Elucidata's expertise and technology, researchers can overcome the challenges of managing and analyzing microarray data, leading to more reliable results and faster advancements in life sciences research.

Contact us to expedite your research journey, or learn more at info@elucidata.io.

‍