Question: What is difference between bulk RNAseq and mRNAseq?
0
gravatar for SupBioInformatics
3 months ago by
SupBioInformatics10 wrote:

Hi,

I was applying jobs and one employer asked if my data is the bulk RNAseq or RNAseq. I am relative new to bioinformatics and I was confused what is the difference between bulk RNA and normal RNA seq. The raw data I used it fastq file, but I started with the count matrix and did some downstream analysis, like DEG, pathway analysis, etc.

I do not know if my data is RNAseq or bulk RNAseq. Can anyone give an example of bulk RNAseq?

Thank you so much.

rna-seq bulk • 313 views
ADD COMMENTlink modified 3 months ago by lieven.sterck9.1k • written 3 months ago by SupBioInformatics10

The employer didn't know that 'bulk RNAseq' and 'RNAseq' mean the same thing.

ADD REPLYlink written 3 months ago by Devon Ryan97k
7
gravatar for GenoMax
3 months ago by
GenoMax92k
United States
GenoMax92k wrote:

Distinction is generally made between RNAseq based on whether data came from a single cells (scRNAseq) or from a sample that contained multiple cells/tissue etc (bulk RNAseq).

Edit: When no special effort is made to isolate single cells (or a group of defined cells) that experiment is normal RNAseq. Bulk designation is not-scientific and signifies size rather than non-specificity.

Total RNA seq refers to technique where entire RNA (including ribosomal RNA which comprises of over 95% of cellular RNA) is made into libraries that are sequenced. mRNAseq would refer to techniques where an attempt is made to selectively retrieve poly-A RNA or actively remove rRNA using complimentary probes so non-rRNA transcripts are enriched.

Majority of the data you are going to find is bulk RNAseq. Single cell RNAseq datasets are now gaining popularity but are still a much smaller fraction of overall data that is publicly available. Single cell RNAseq tends to sample only 10-20% of transciptome and there is a 3'-end bias for many methods.

ADD COMMENTlink modified 3 months ago • written 3 months ago by GenoMax92k

Bulk Rna-seq is a more commonly used term to refer to a sample of sorted cells (using FACS) to select a more homogeneous cell population than using a tissue slice for RNA extraction.

ADD REPLYlink written 3 months ago by tiago2112871.2k

While bulk RNA-seq can certainly be done on sorted cells, it is not a requirement. But it helps to clean up the signal for sure

ADD REPLYlink written 3 months ago by Friederike6.5k

Cell sorting is rather uncommon with bulk RNA-seq. Most commonly people perform RNA extraction on whole tissues or cell culture dishes.

ADD REPLYlink written 3 months ago by Devon Ryan97k

I guess I am in a bubble then. 99% of RNA-Seq is made out of sorted cells on my planet, and we called it Bulk RNA-Seq. RNA-Seq obtained from entire tissues is referred to as just RNA-Seq. But I guess it makes sense that Bulk could also be referred to tissue, although I have associated Bulk as a more clean RNA-Seq with homogenous cells with the years. Terminology wars.

ADD REPLYlink modified 3 months ago • written 3 months ago by tiago2112871.2k
1
gravatar for lieven.sterck
3 months ago by
lieven.sterck9.1k
VIB, Ghent, Belgium
lieven.sterck9.1k wrote:

for me this is as follows:

bulk RNAseq is when you extract all kinds of RNA sequences from the cell/tissue/organism, thus without doing any filtering or enrichment. This sample will include different kinds of RNA: mRNA, lncRNA, miRNA, snoRNA ....

(m)RNAseq, is when you applied some filtering on the RNA you extracted: usually this is capture by poly-T beads for instance, which will result in an RNA samples that has mostly mRNA sequences in it (due to the presence of a poly-A tail)

ADD COMMENTlink modified 3 months ago • written 3 months ago by lieven.sterck9.1k
2

Bulk RNA-seq is typically used to differentiate between bulk and single-cell as described by Genomax. What you're referring to here would probably be considered "total RNA-seq" vs. "ribo-depleted" vs. "poly(A)-enriched" vs. any other enrichment method

ADD REPLYlink written 3 months ago by Friederike6.5k

I see, thx Friederike

On the other hand if I had to refer to single cell RNAseq, I would use the term scRNAseq ...

Anyway, if we're not confused by the data itself we'll confuse ourself with the naming :)

ADD REPLYlink written 3 months ago by lieven.sterck9.1k
1

oh, for sure, there must have been another level of miscommunication. Plus none of these terms are really fixed. I actually think it's more likely that the interviewer was interested in distinguishing between total and mRNA-seq enrichments rather than bulk RNA-seq vs. single-cell RNA-seq

ADD REPLYlink written 3 months ago by Friederike6.5k
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