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Constructing a cDNA Library for Next-Generation Sequencing: A Step-by-Step Guide

Written by Carl Swanson | Jul 10, 2023 1:26:26 PM

Next-generation sequencing (NGS) has revolutionized the field of genomics, enabling high-throughput sequencing of entire genomes. To study gene expression or sequence RNA molecules using NGS, one first needs to construct a complementary DNA (cDNA) library. This article will guide you through the steps required to create a cDNA library for next-generation sequencing.

Isolation of RNA

The first step in creating a cDNA library is the isolation of RNA from the cells or tissues of interest. The method used for RNA extraction depends on the type of sample and can range from commercially available kits to traditional methods like phenol-chloroform extraction. It's crucial to ensure that the RNA is of high quality and free from contaminants, as these could interfere with subsequent steps.

Selection of RNA Molecules

Depending on the research question, you might want to sequence all RNA molecules (total RNA-seq) or only a specific subset, like messenger RNA (mRNA-seq) or small RNAs (small RNA-seq). For mRNA-seq, poly(A) selection or ribosomal RNA depletion can be used to enrich for mRNA molecules. For small RNA-seq, size selection can be performed using gel electrophoresis or specialized kits.

Reverse Transcription

Once the desired RNA molecules are isolated, they are reverse transcribed into cDNA using reverse transcriptase. This enzyme uses an RNA template to synthesize a complementary DNA strand. Depending on the type of RNA being sequenced, different primers are used for reverse transcription. For example, oligo(dT) primers are used for mRNA, while specific stem-loop primers are used for microRNAs.

Second Strand Synthesis and Purification

After reverse transcription, the second DNA strand is synthesized to create double-stranded cDNA. This is typically done using DNA Polymerase I and RNase H, which degrade the RNA template and fill in the complementary DNA strand. The resulting double-stranded cDNA is then purified to remove enzymes and other reaction components.

Fragmentation and Adapter Ligation

The purified cDNA is fragmented into smaller pieces suitable for sequencing. This can be done using mechanical shearing or enzymatic fragmentation. After fragmentation, platform-specific adapters are ligated to the ends of the cDNA fragments. These adapters allow the fragments to bind to the sequencing flow cell and also contain sequences necessary for amplification and sequencing.

Amplification and Quality Control

The adapter-ligated cDNA fragments are amplified using PCR to generate sufficient material for sequencing. Following amplification, it's important to perform quality control checks to ensure the library is of good quality. This usually involves checking the size distribution of the library fragments and quantifying the library to ensure there is enough material for sequencing.

Creating a cDNA library for next-generation sequencing involves several carefully orchestrated steps, from RNA isolation to library amplification. Each step must be performed with precision and accuracy to ensure the resulting library is of high quality and suitable for sequencing. With a well-prepared cDNA library, researchers can uncover the depth and complexity of the transcriptome, advancing our understanding of gene expression and its role in health and disease.