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RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

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Related Experiment Video

Updated: Aug 10, 2025

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel

Published on: April 20, 2018

Whole Genome Wide SSR Markers Identification Based on ddRADseq Data.

Gitanjali Tandon¹, Sarika Jaiswal¹, Mir Asif Iquebal²

¹Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India.

Methods in Molecular Biology (Clifton, N.J.)

|February 13, 2023

Summary

Advanced sequencing technologies generate vast data for discovering genetic markers like simple sequence repeats (SSRs). These SSR markers, mined from ddRADseq data, are crucial for diversity analysis and developing new crop varieties.

Keywords:

MISA QDD SSR markers STACKS consensus sequences ddRADseq

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

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Last Updated: Aug 10, 2025

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel

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Published on: April 20, 2018

DamID-seq: Genome-wide Mapping of Protein-DNA Interactions by High Throughput Sequencing of Adenine-methylated DNA Fragments

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High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

High-throughput Identification of Gene Regulatory Sequences Using Next-generation Sequencing of Circular Chromosome Conformation Capture 4C-seq

Published on: October 5, 2018

Area of Science:

Genomics and Bioinformatics
Molecular Biology
Plant Breeding

Background:

Next-generation sequencing (NGS) technologies produce large volumes of sequence data.
Genetic markers such as SSRs, SNPs, and InDels are vital for genetic studies and breeding.
Microsatellite Simple Sequence Repeat (SSR) markers possess ideal properties for genetic analysis.

Purpose of the Study:

To explore the utility of ddRADseq data for mining microsatellite SSR markers.
To facilitate diversity analysis and the development of new varieties with desired traits using SSR markers.

Main Methods:

Assembly of ddRADseq data into consensus sequences using the STACKS program.
Mining of microsatellite SSRs from assembled sequences using QDD and MISA tools.

Main Results:

Successful extraction of microsatellite SSR markers from ddRADseq data.
Demonstration of SSR markers' suitability for genetic diversity studies.

Conclusions:

ddRADseq data is a valuable resource for discovering SSR markers.
The identified SSR markers can significantly aid researchers and breeders in genetic diversity assessment and crop improvement.