The main objective of this study is to evaluate and compare the detection of pseudouridine (Ψ) modifications at the gene level in lung cells, using two different sequencing platforms: Nanopore direct RNA sequencing and BID‑Seq.
In this experiment, lung cells were treated under two conditions:
Control: Lung cells cultured in standard media (media-only).
PM Exposure: Lung cells exposed to urban particulate matter at 125 µg/mL for 24 hours.
This experimental setup aims to simulate an environmental stress scenario where PM exposure is known to induce cellular stress responses.
Our hypothesis is that pseudouridine modifications, which are critical for RNA stability and function, may vary in response to this exposure.
By comparing the results from both sequencing methods, we hope to determine:
Which genes are marked as pseudouridine-modified in each condition?
To what extent the two platforms agree on the modified genes under PM exposure versus control.
The biases inherent in each method and whether one method is more sensitive or specific under these experimental conditions.