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Related Experiment Video

Updated: Feb 28, 2026

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

'PACLIMS': a component LIM system for high-throughput functional genomic analysis.

Nicole Donofrio¹, Ravi Rajagopalon, Douglas Brown

¹Department of Plant Pathology, Fungal Genomics Laboratory, North Carolina State University, Raleigh, NC, USA. ndonofr@unity.ncsu.edu

BMC Bioinformatics

|April 14, 2005

Summary

This summary is machine-generated.

A new platform, PACLIMS, aids in tracking biological materials and data for genome-wide functional annotation of the rice blast fungus (Magnaporthe grisea). This high throughput system supports mutational analysis for gene function discovery.

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Last Updated: Feb 28, 2026

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Area of Science:

Genomics
Mycology
Bioinformatics

Background:

Advances in sequencing technology generate vast eukaryotic genomes.
Computational tools aid gene annotation but require biological validation.
Functional gene annotation necessitates experimental support, such as mutational analysis.

Purpose of the Study:

To develop an effective platform for tracking biological materials and data in genome-wide functional annotation projects.
To support a high throughput pipeline for generating and analyzing random insertion mutants of Magnaporthe grisea.

Main Methods:

Designed and implemented the Platform for Automated Collection and Tracking of LIMS (PACLIMS).
Integrated barcode and scanner technology for simplified data entry and reduced human error.
Developed the platform in conjunction with experimental protocols for standardized mutant generation and phenotypic assays.

Main Results:

The PACLIMS platform efficiently supports the generation of 50,000 random insertion mutants of Magnaporthe grisea.
PACLIMS is user-friendly, modifiable, and cost-efficient for materials and data tracking.
The platform ensures consistent handling of mutants and comprehensive data capture throughout the research process.

Conclusions:

Computational gene annotation requires biological validation, increasing the need for high throughput analysis platforms.
PACLIMS provides a robust solution for genome-wide mutational analyses.
The design principles of PACLIMS can serve as a model for other high throughput mutational studies.