Category: Transcriptomics
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How to Analyze RNAseq Data for Absolute Beginners Part 20: Comparing limma, DESeq2, and edgeR in Differential Expression Analysis
Introduction Differential expression (DE) analysis represents a fundamental step in understanding how genes respond to different biological conditions. When we perform RNA sequencing, we’re essentially taking a snapshot of all the genes that are active (or expressed) in our samples at a given moment. However, the real biological insights come from understanding how these expression…
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How to Analyze RNAseq Data for Absolute Beginners Part 19: Understanding RNA-Seq Gene Expression Normalization
Introduction: Why Normalization Matters in RNA-Seq Analysis RNA sequencing (RNA-seq) has revolutionized our ability to measure gene expression, but the raw data needs careful processing to yield meaningful biological insights. In this comprehensive guide, we’ll explore why normalization is crucial and how to convert between different expression metrics using R. Building on our previous tutorials…
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How to Analyze RNAseq Data for Absolute Beginners Part 18: Analyzing Viral Gene Expression in Host RNA-seq Data
Understanding viral gene expression patterns during infection is crucial for studying host-pathogen interactions. This comprehensive guide will walk you through the process of accurately quantifying viral transcripts from RNA-seq data of infected host cells, providing you with practical approaches for this challenging analysis. The Challenge of Viral RNA-seq Analysis When we sequence RNA from virus-infected…
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How to Analyze RNAseq Data for Absolute Beginners Part 17: Viral Sequence Detection
Introduction to Viral Sequence Detection The intersection of high-throughput sequencing and viral genomics has transformed our understanding of viral biology and disease. Through RNA-seq and whole-genome sequencing (WGS), researchers can now peer into the complex relationship between viruses and their hosts with unprecedented clarity. This technological breakthrough has revolutionized both biomedical research and clinical diagnostics,…
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How to Analyze RNAseq Data for Absolute Beginners Part 16: A Comprehensive Tutorial on Identifying Fusion Genes
Understanding Fusion Genes: Key Concepts for Cancer Research What Are Fusion Genes and Why Do They Matter? Fusion genes represent a fascinating phenomenon in cancer biology where two previously separate genes join together, often creating proteins with altered or entirely new functions. These genetic mergers typically arise through chromosomal rearrangements like translocations, deletions, or inversions.…
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How to Analyze RNAseq Data for Absolute Beginners Part 15-2: Mastering UMI-Based miRNA-Seq Analysis
Understanding UMI-Based miRNA Sequencing MicroRNAs (miRNAs) serve as crucial regulators in gene expression, making their accurate quantification essential for understanding disease mechanisms and biological processes. While traditional miRNA sequencing has proven valuable, the integration of Unique Molecular Identifiers (UMIs) represents a significant advancement in achieving precise miRNA measurements. This tutorial will guide you through the…
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How to Analyze RNAseq Data for Absolute Beginners Part 15: A Complete Guide to miRNA-seq Analysis
Understanding the World of microRNAs The fascinating world of microRNAs (miRNAs) represents one of molecular biology’s most elegant regulatory systems. These tiny RNA molecules, spanning just 20-24 nucleotides, function as precise genetic regulators by binding to messenger RNAs (mRNAs) and fine-tuning their expression. Since their serendipitous discovery in the early 1990s, miRNAs have revolutionized our…
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How to Analyze RNAseq Data for Absolute Beginners Part 14: Mastering Small RNA-Seq Analysis
The Hidden World of Small RNAs: More Than Just Tiny Molecules Small RNAs are fascinating molecules that challenge the traditional “DNA to RNA to protein” dogma of molecular biology. Despite being just 20-30 nucleotides in length – barely a fraction of a typical messenger RNA – these molecules orchestrate complex biological processes with remarkable precision.…
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How to Analyze RNAseq Data for Absolute Beginners Part 13: Circular RNAseq Analysis
Understanding the Biology of Circular RNAs The Nature of Circular RNAs Circular RNAs (circRNAs) represent one of molecular biology’s most fascinating discoveries. Unlike the linear RNA molecules that dominated our understanding of gene expression for decades, circRNAs form continuous loops through a unique process called back-splicing. In this process, a downstream 5′ splice site connects…
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How to Analyze RNAseq Data for Absolute Beginners Part 11: Mastering Transcript-Level Alternative Splicing Analysis
Video Tutorial From Gene-Level to Transcript-Level Analysis In our previous exploration of gene-level splicing analysis, we laid the groundwork for understanding how alternative splicing shapes gene expression. Now, we’re taking a deeper dive into the fascinating world of transcript-level analysis, where we can uncover the intricate details of how genes produce different protein variants through…
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Recent Posts
- How to Analyze RNAseq Data for Absolute Beginners Part 20: Comparing limma, DESeq2, and edgeR in Differential Expression Analysis
- How to Analyze RNAseq Data for Absolute Beginners Part 19: Understanding RNA-Seq Gene Expression Normalization
- How to Analyze RNAseq Data for Absolute Beginners Part 18: Analyzing Viral Gene Expression in Host RNA-seq Data
- How to Analyze RNAseq Data for Absolute Beginners Part 17: Viral Sequence Detection
Tags
Alternative Splicing Analysis Cancer cell-type composition CIBERSORTx circRNA-seq circular RNA Differential Expression Fusion Gene Detection gene expression immune cell profiling Isoform limma microRNA miRNA miRNA-seq NCBI GEO Normalization PAM50 Quantification RNA Editing Salmon small RNA smRNA smRNA-seq TPM Transcript UMI Virus Virus-Host Virus Gene Expression