---
title: "Mapping and quantifying mammalian transcriptomes by RNA-Seq"
authors: ["Mortazavi A", "Williams BA", "McCue K"]
year: 2008
journal: Nature Methods
type: paper
tags: [rna-seq, transcriptomics, sequencing]
cited_by: 12000
impact: foundational
---

# Mapping and quantifying mammalian transcriptomes by RNA-Seq

## Summary

Introduced RNA-Seq methodology for comprehensive transcriptome analysis. [[Defined]] [[RPKM Normalization]] and [[Established]] [[Best Practices]] for gene expression quantification.

## [[Key Findings]]

- **RPKM normalization**: [[Reads Per Kilobase Million]] for cross-[[Sample]] comparison
- **Dynamic range**: 5 orders of magnitude vs microarray's 3
- **Isoform [[Detection]]**: Can distinguish splice variants

## Methodology

[[High-Throughput Sequencing]] applied to [[cDNA Libraries]]. [[Developed]] [[RPKM Normalization]] method still used today.

## Relevance to My Work

Core methodology for [[Single-Cell RNA-Seq Analysis]] experiments. [[RPKM Normalization]] [[Used In]] [[Experiment-2024-11-15]].

## [[Related Work]]

- Foundation for [[Tang2009-Single-Cell-RNA-Seq]]
- Methods used in [[Trapnell2010-TopHat]]
