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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 microarray-based...

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Updated: Jun 3, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

PAGD: the Persea americana Genome Database and a Docker-based transcriptome analysis workflow.

Siyi Ma^1,2, Huadong Feng², Danni Yang³

¹Institute of International Rivers and Eco-security, Yunnan University, Kunming, Yunnan, 650091, China.

|June 2, 2026

Summary

This summary is machine-generated.

The Persea americana Genome Database (PAGD) integrates avocado genome assemblies and transcriptomic data. This platform offers pre-computed analyses and reproducible workflows for enhanced avocado research.

Keywords:

Persea americana Database Docker Drupal Snakemake Transcriptome Tripal

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Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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Last Updated: Jun 3, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

Published on: March 5, 2022

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

Area of Science:

Genomics
Bioinformatics
Plant Science

Background:

Avocado (Persea americana) is a significant global fruit crop.
Existing genomic resources are fragmented and lack integrated multi-omics analyses.
A need exists for a unified platform for avocado genomic data.

Purpose of the Study:

To develop an integrated platform for avocado genomic and transcriptomic data.
To provide pre-computed multi-omics analyses and reproducible workflows.
To facilitate functional genomics, breeding, and comparative studies in avocado.

Main Methods:

Consolidated two high-quality avocado genome assemblies (Hass and West Indian).
Integrated RNA-seq datasets from 13 NCBI BioProjects with uniform reprocessing and metadata.
Developed Docker-encapsulated Snakemake workflows for transcriptome analysis.

Main Results:

Launched the Persea americana Genome Database (PAGD) with integrated multi-omics data.
PAGD includes gene family classification, collinearity, gene density, and expression profiles.
Provided tools like BLAST, JBrowse, interactive heatmaps, and data download.

Conclusions:

PAGD enhances avocado genomic resources through data integration and reproducible workflows.
The platform lowers the technical barrier for RNA-seq analysis.
PAGD supports diverse applications in plant science, breeding, and comparative genomics.