Which RNA type I should considered as long non-coding RNAs

Question

[zizigolu]

Hello

We have exosome-sequensing (from plasma). In raw read counts file, I see 72650 gene names.

This is how my read count file looks like

I have created a percentage bar chart for categories of RNAs annotated in this exosome-seq like

Which category (RNA type) I should consider as long non-coding RNA (lncRNA) ?

Can I consider this observed24% Long intergenic non-coding RNA (lincRNA) (sense+antisense) as long non-coding RNA (lncRNA) ?

But as I read Generally speaking we don’t expect much lncRNA/mRNA in plasma and much of that will be heavily fragmented which makes it very difficult to sequence. So how I see 24% of lincRNAs ?

If this was your data, which type of RNAs here you would considered as long non-coding RNA (lncRNA) ?

Thanks for any intuition

[GenoMax]

Which category (RNA type) I should consider as long non-coding RNA (lncRNA) ?

What ever is annotated as lncRNA at RNAcentral. Download the lncRNA's for your organism and cross check the identifiers in your list.

[zizigolu]

Thank you so much

I see this

In rfam part I could not find any lncRNAs

Am I right in searching?

[GenoMax]

If you use the search link I provided above you can narrow down the genome you are interested in and then use the Download button at top right to download the filtered data. e.g. these are lncRNA for mouse.

[zizigolu]

Yes, thank you so much

Now I am following you

I downloaded the results from my search

The file looks like this. For instance, by searching for URS00000E9EFC_9606 , in my raw read counts I will see MUC5B

Is there anyway to download the results as the identifier in my raw read counts or I should convert what I have downloaded to my identifiers?

[GenoMax]

Better than that get this file that maps GENCODE ids.

URS0000000055   GENCODE ENST00000585414 9606    lncRNA  ZNF451-AS1
URS00000000C9   GENCODE ENST00000514011 9606    lncRNA  MEF2C-AS1
URS00000000FD   GENCODE ENST00000448543 9606    lncRNA  LINC01937
URS0000000351   GENCODE ENST00000452009 9606    lncRNA
URS00000005D1   GENCODE ENST00000563639 9606    lncRNA
URS0000000787   GENCODE ENST00000452952 9606    lncRNA  FAM230H
URS0000000AA1   GENCODE ENST00000615750 9606    lncRNA  CCL3-AS1

AS1 in gene names stands for anti-sense RNA.

Leaving this as a future reference: There is an id_mapping file in this directory that should help.

[zizigolu]

Thank you so much GenoMax

My boss has asked me is there any RNA in my exosome-seq

I supposed he means mRNA

If so how I know from 72650 identifiers in my raw read counts which ones are RNA (mRNA) ?

[GenoMax]

If you are analyzing mRNA sequence data then you should only see mRNA's. I don't understand the question since your raw counts are for genes for which there was annotation.

Note: Kit used for the prep may be relevant to check on.

[zizigolu]

Thank you so much GenoMax actually you resolved my question throughly

I got a question which I was not able to solve yet

If I am only interested lncRNAs related to Angiogenesis GO term how to download such a list please?

I searched for Angiogenesis in search bar and some results came and I see for instance 123 of lncRNAs are here and I want to download them

[zizigolu]

Sorry GenoMax I got another question please

How I can add GO annotation filter to my downloads?

I mean only downloading ncRNA having GO annotation

[Renesh]

Other quick way is to check the length of RNA. The lncRNA generally is > 200 nt in length. This article may help you to identify and filter lncRNA from your dataset

[zizigolu]

It is really confusing by length, when I subtracted start from stop, I obtained more than 80% of my data longer than 200 nt while my exosomes is from plasma and I don't expect too many lncRNAs