Multiomics Analysis FAQ

• • How Can Gene Expression Levels of Specific Genes Be Quantified Across Different Species in Transcriptome Sequencing?

  To quantify the expression levels of specific genes across different species, the following approach can be applied:   1. Quality Control and Data Cleaning Begin by assessing the raw sequencing data (FASTQ files) using quality control tools such as FastQC to evaluate sequencing quality, duplication levels, adaptor contamination, and other technical artifacts.   Based on the quality reports, employ sequence trimming tools like Trimmomatic or cutadapt to remove low-quality sequences, adaptors, and other......

• • Can Saccharomyces cerevisiae S288C Be Used as the Reference Genome for Transcriptome Sequencing of the BY4741 Strain?

  BY4741 and S288C are both commonly used laboratory strains of Saccharomyces cerevisiae. S288C is the reference strain of yeast, with its genome being the first to be fully sequenced, and it is widely used as a reference in various genomic tools and databases. BY4741, on the other hand, is a haploid strain derived from S288C and is frequently employed in genomic studies, including gene knockout experiments.   If you are conducting transcriptome sequencing (RNA-Seq) and require a reference genome for al......

• • What Are the Major Applications of RNA Sequencing (RNA-seq) in Biological and Medical Research?

  RNA sequencing (RNA-seq) is a powerful and widely adopted technique with broad applications across various domains of biological and medical research. Below are several key application areas of RNA-seq:   Gene Expression Profiling RNA-seq enables the quantification of gene expression across different biological samples or experimental conditions, facilitating the investigation of transcriptional regulation and the identification of genes with condition-specific expression changes.   Differential Gene ......

• • What Distinguishes Unigene from CDS in Eukaryotic De Novo Transcriptome Assembly?

  In eukaryotic de novo transcriptome assembly, the terms “Unigene” and “CDS” refer to distinct biological concepts and data entities, each serving different analytical purposes.   Unigene A Unigene typically represents a non-redundant set of assembled transcripts derived from RNA sequencing data. It is often constructed by clustering expressed sequence tags (ESTs) or mRNA sequences originating from the same gene locus. The Unigene concept is also associated with databases that integrate and classify su......

• • How Can Genomic, Transcriptomic, Proteomic, and Metabolomic Data Be Effectively Integrated?

  Integrating multi-omics datasets—including genomic, transcriptomic, proteomic, and metabolomic data—is a complex but increasingly essential task in systems biology. The following outlines a systematic approach and key steps for effective integration:   Define the Research Objective and Biological Question The first step in multi-omics integration is to clearly identify the research goal, which directly influences the integration strategy:   1. Disease Mechanism Elucidation Focuses on analyzing cross-t......

• • What Experimental Approaches Can Be Performed Following Transcriptome Sequencing?

  Transcriptome sequencing (RNA-seq) is a powerful technology for investigating gene expression. The data generated from RNA-seq can be utilized for a wide range of downstream analyses and experimental designs, including:   Differential Gene Expression Analysis This is one of the most commonly conducted analyses. Researchers compare transcriptomes under different conditions or treatments (e.g., disease vs. healthy, or treated vs. control) to identify genes that exhibit significant differences in express......

• • How Long Can Tissue Samples Be Stored at −20°C Prior to Transcriptomic and Metabolomic Analyses?

  For transcriptomic and metabolomic analyses, tissue samples should ideally not be stored at −20°C for longer than six months. Extended storage is recommended at −80°C to better preserve the integrity of RNA and the stability of metabolites.   MtoZ Biolabs, an integrated chromatography and mass spectrometry (MS) services provider. Related Services Integrative Transcriptomics-Metabolomics Analysis Service

• • How Can Transcriptome Sequencing Data Be Submitted to the GEO Database?

  The submission of transcriptome sequencing data to the Gene Expression Omnibus (GEO) involves several essential steps, outlined as follows:   Register a GEO Account Before submitting data, you must register for a GEO account. This can be done by visiting the GEO website and clicking on the "Register" button to create an account.   Create a GEO Series After logging into your account, initiate a new GEO Series to house your transcriptome sequencing data. Click the “Submit” button and select the “New GEO......

• • What Are the Next Steps After Differential Gene Expression Analysis Without KEGG or GO Enrichment in Transcriptome Studies?

  After completing transcriptome sequencing and performing only differential gene expression (DGE) analysis without conducting KEGG or Gene Ontology (GO) enrichment analysis, several subsequent steps can be considered to gain deeper biological insights:   1. Interpret the Biological Significance of Differentially Expressed Genes (DEGs) The first step involves interpreting the biological roles of the identified DEGs. This can be achieved by consulting relevant literature and databases to explore the func......

• • How Should Transcriptome Sequencing Data Be Processed and Analyzed?

  Following transcriptome sequencing, a large volume of transcriptomic data is typically generated. To extract biologically meaningful insights, a series of analytical steps must be conducted, including the following:   1. Quality Control of Sequencing Data Ensuring the accuracy and reliability of sequencing data is the first step. This involves assessing sequencing quality scores, removing low-quality bases, eliminating adapter sequences, and filtering reads containing ambiguous nucleotides.   2. Prepr......