Identification of novel lncRNA by reanalysis of RNA-seq data in Zika Virus Infected hiNPCs

Venkatesan, Amouda; Barik, Aishwarya; Paul, Dahrii; Venkatesan, Amouda; Das, Rajesh

doi:10.1007/s13337-022-00771-1

Cited by 2 publications

(1 citation statement)

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“…Bedtools [ 28 ] (v2.30.0) was used to identify cis-target genes for DE lncRNAs. Neighbouring genes within 100,000 bp of DE lncRNAs were considered cis-target genes of the lncRNAs [ 29 ]. The Pearson correlation coefficient method [ 30 ] was used to predict trans-target genes.…”

Section: Methodsmentioning

confidence: 99%

Identification and functional prediction of long non-coding RNAs related to oxidative stress in the jejunum of piglets

Li,

Zhang,

Jin

et al. 2024

Anim Biosci

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Objective: Oxidative stress (OS) is a pathological process arising from the excessive production of free radicals in the body. It has the potential to alter animal gene expression and cause damage to the jejunum. However, there have been few reports of changes in the expression of long noncoding RNAs (lncRNAs) in the jejunum in piglets under OS. The purpose of this research was to examine how lncRNAs in piglet jejunum change under OS.Methods: The abdominal cavities of piglets were injected with diquat (DQ) to produce OS. Raw reads were downloaded from the SRA database. RNA-seq was utilized to study the expression of lncRNAs in piglets under OS. Additionally, six randomly selected lncRNAs were verified using quantitative real-time polymerase chain reaction (qRT‒PCR) to examine the mechanism of oxidative damage.Results: A total of 79 lncRNAs were differentially expressed (DE) in the treatment group compared to the negative control group. The target genes of DE lncRNAs were enriched in gene ontology (GO) terms and Kyoto encyclopedia of genes and genomes (KEGG) signaling pathways. Chemical carcinogenesis-reactive oxygen species, the Foxo signaling pathway, colorectal cancer, and the AMPK signaling pathway were all linked to OS.Conclusion: Our results demonstrated that DQ-induced OS causes differential expression of lncRNAs, laying the groundwork for future research into the processes involved in the jejunum’s response to OS.

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Section: Methodsmentioning

confidence: 99%