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