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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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Evaluation of noninvasive biospecimens for transcriptome studies.

Molly Martorella^1,2, Silva Kasela^3,4, Renee Garcia-Flores^3,5,6

¹New York Genome Center, New York, NY, USA. mem2331@cumc.columbia.edu.

|December 20, 2023

Summary

Noninvasive biospecimens like hair follicles and urine pellets offer consistent quality for transcriptomic studies. These tissues enable longitudinal designs and disease-relevant discovery, expanding research possibilities.

Keywords:

EQTLs Hair follicles Methods Noninvasive RNA-sequencing Transcriptomics Urine cell pellets

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Area of Science:

Genomics
Molecular Biology
Biotechnology

Background:

Transcriptome studies are crucial for understanding gene regulation and disease biology.
Current tissue collection methods are often limited to single timepoints or blood-based cell types.
Noninvasive tissues offer potential for longitudinal studies, diverse cell types, and larger sample sizes.

Purpose of the Study:

To develop and evaluate methods for sampling noninvasive biospecimens for transcriptomics.
To characterize the biological and technical features of these noninvasive samples.
To assess the feasibility of using noninvasive tissues in transcriptomic and clinical applications.

Main Methods:

Collected buccal swabs, hair follicles, saliva, and urine cell pellets from 19 individuals over multiple timepoints.
Prepared 472 transcriptomes using three different library preparations.
Analyzed sample quality, cell types, expression profiles, and performance in disease-relevant applications.

Main Results:

Hair follicles and urine cell pellets demonstrated the most promise among the four noninvasive tissues studied.
These tissues showed consistent sample quality, relevant cell types, and expression profiles.
Demonstrated successful application in a variety of transcriptomic and clinical analyses.

Conclusions:

Noninvasive biospecimens, particularly hair follicles and urine cell pellets, are valuable for transcriptomic research.
These tissues facilitate longitudinal study designs and disease-relevant discovery.
This study provides a framework for utilizing noninvasive samples in future clinical applications and research.