How to analyze differentially expressed lncRNA from total RNA

Question

[ta_awwad]

Hello everyone, I have RNA-seq data and I would like to detect differentially expressed lncRNA with DESeq2, does anyone have analysis workflow to follow? thanks much Tamer

Answer 1

[WouterDeCoster]

I think the most appropriate method is to analyse the data just like you would for all RNA-seq, and filter out the lncRNAs after you get the differentially expressed genes from the full analysis. Preselecting genes will only bias your results.

[ta_awwad]

Thanks much, do you know by any chance how to get a list of lncRNA transcript (from phantom project ) or I should rely on UCSC lincRNA table? moreover, do you have R code for the filtering step?

thanks much

[BioinfGuru]

Ensembl Biomart allows you to download what you need.

First: select what is needed e.g. Dataset: Ensembl 89 + then choose species --> Filter: gene type --> lincRNA --> Attributes: Gene ID, Gene Name, Gene Type

Second: Click "results"

Third: Export all results to TSV --> Go

[WouterDeCoster]

I'd think the default UCSC/Ensembl annotation will contain already a bunch of lncRNAs, you could complement these if you like with e.g. Lncipedia data.

moreover, do you have R code for the filtering step?

That's quite basic R, see for example here

[Arindam Ghosh]

During RNA-seq data analysis, reads may get aligned to different types of transcripts including mRNA, lncRNA, miRnA etc. However, there may be some artifacts in these alignments. For example, ncRNA should not exist in polyA enrich samples. How do we identify these false mappings? Or is it just based on empirical knowledge?

[WouterDeCoster]

LncRNAs are often polyadenylated.

Answer 2

[EagleEye]

Check this post for workflow

A: Any One please provide protocol for Analysing long noncoding RNA illumina NGS da

Ad for R Differential Expression steps in R,

A: Differential gene expression using R studio