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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...

Real Time RT-PCR

Real Time RT-PCR

Real-time reverse transcription-polymerase chain reaction, or Real-time RT-PCR, is an analytical tool used to determine the expression level of target genes. The method involves converting mRNA to complementary DNA with the help of an enzyme known as reverse transcriptase, followed by the PCR amplification of the cDNA. These two processes can be performed simultaneously in a single tube or separately as a two-step reaction.
The real-time quantification of the number of amplified products is...

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Related Experiment Video

Updated: Oct 21, 2025

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

Published on: June 30, 2023

Variant abundance estimation for SARS-CoV-2 in wastewater using RNA-Seq quantification.

Jasmijn A Baaijens¹, Alessandro Zulli², Isabel M Ott³

¹Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.

Medrxiv : the Preprint Server for Health Sciences

|September 8, 2021

Summary

This summary is machine-generated.

Wastewater sequencing effectively estimates SARS-CoV-2 variant prevalence, complementing clinical surveillance. This method tracks variant trends, especially when clinical data is limited.

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Quantification and Whole Genome Characterization of SARS-CoV-2 RNA in Wastewater and Air Samples

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Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR

Simultaneous DNA-RNA Extraction from Coastal Sediments and Quantification of 16S rRNA Genes and Transcripts by Real-time PCR

Published on: June 11, 2016

Area of Science:

Environmental microbiology
Virology
Computational biology

Background:

Monitoring SARS-CoV-2 variants is crucial for pandemic control.
Wastewater surveillance offers an efficient proxy for COVID-19 population rates.
Accurately predicting variant proportions in wastewater presents significant challenges.

Approach:

Sequencing SARS-CoV-2 RNA from wastewater samples.
Applying computational RNA-Seq quantification methods to estimate variant abundance.
Validating results by comparing wastewater data with clinical isolate sequences.

Key Points:

The study demonstrates wastewater sequencing can estimate variant abundances.
Temporal dynamics of SARS-CoV-2 variants in wastewater broadly align with clinical data.
The technique shows high sample variability and limited detection of low-frequency variants (<10%).

Conclusions:

Wastewater sequencing provides a viable method for monitoring SARS-CoV-2 variant trends.
This approach is particularly useful in settings lacking widespread clinical sequencing.
While less sensitive than clinical sequencing, wastewater surveillance offers valuable population-level insights.