What exactly is RNA-seq probe?

Question

[ConvolutedGenome]

Hi all,

I'm a long time lurker, but this is my first post here, so I'm sorry if I do something wrong or post something that is against the rule,

I'm new to RNA-seq analysis. But I've downloaded a huge dataset with matched RNA-seq and Genotype data with the goal of calling eQTLs.

I've been reading the documentation that came with the dataset, and there is a quote that confused me regarding the RNA-seq dataset, it says the following:

"Expression data are from GRCH37 RNAseq probe and packed in the folder marked as xxxx.expression-data-matrixfmt.RNAseq_probe_set_grc37.c1.GRU.tar.gz”."

My question is (sorry if this is a dumb question):

• It says that the expression data is from GRCh37 RNA-seq probe... But what exactly is an RNA-seq probe?

Additional question:

• It seems like the original paper aligned their RNA-seq data to the GRCh37/hg19 reference genome... but my lab is using the GTEx V8 pipeline for eQTL calling... which means that I need to align it to the newest GRCh38 reference genome... is this acceptable? Compounded by the fact that the paper used GRCh37 probe (which I dont entirely understand), I'm just not sure if my pipeline is appropriate for this dataset.

---> For context, my lab wanted to use the GTEx V8 pipeline in order to standardize the analysis to follow the newest GTEx standard so that we can compare our findings to GTEx findings

Thankyou!!

Answer 1

[GenoMax]

Without a reference to the dataset you are referring to this would be hard to answer. It is possible that they used expression microarrays (probe reference) or they are simply referring to genes as RNAseq probes.

[ConvolutedGenome]

I downloaded a dataset of RNA-seq reads and matching genotype, the genotype is from microarray, but the RNA-seq would not be from microarray right? In the paper, they explicitly mention that they sequenced the isolated RNA on HiSeq 2500, which is a sequencing platform!

[GenoMax]

Then thinking naively, the probe reference is simply indicating that the RNAseq data was aligned to GRCh37. Since you have raw data you would be able to align it to GRCh38. Issue could be with genotype data. The locations on SNP chip likely are for GRCh37 as well and you may need to lift those over.

[ConvolutedGenome]

What do you mean by "lift those over"?

Thanks so much dude :')

[GenoMax]

Translate coordinates from one genome build to other.

[ConvolutedGenome]

Thanks dude, you are a life-saver :)))))