I want to use ROSMAP genotype data with corresponding expression data for eQTL analysis. But what I'm confused is which expression data should I choose? And how to get it?
I find expression data online at "https://www.synapse.org/#!Synapse:syn3800853"? Can I use this data(ROSMAP_arrayExpression_normalized.tsv) directly for eQTL analysis?
Created by xiaoyan li adelalady @adelalady-
I suspect you want the "gene" level data, rather than the "isoform" level data. Unless you want to apply your own normalization, you probably want the "normalized" files. There are 2 of them, because they were normalized in 2 batches. As for the methods for the eQTL on the xQTL Server, the manuscript should contain those details, and there is contact information on the xQTL Server website. We do not maintain it, so cannot provide details about it's contents.
If you want to generate your own there are 1000 Genomes imputed data available through this repository in addition to the assayed genotypes.
Solly Dear Solveig,
Thank you for your reply~
And there are six subfiles under this folder(syn3388564) about RNA sequence data, which one should I choose to do the eQTL analysis with genotype data?
Yes, I have also downloaded eQTL results online(http://mostafavilab.stat.ubc.ca/xQTLServe/), and another question is that whether the results of the eQTL analysis used imputed genotype data as input genotype data? If so, then I can use the eQTL results directly.
I'm really sorry to bother you.
Thanks so much and have a nice day.
Best,
XiaoYan @adelalady-
Per the first sentence of the abstract "We report a multi-omic resource generated by applying quantitative trait locus (xQTL) analyses to RNA sequence, DNA methylation and histone acetylation data from the dorsolateral prefrontal cortex of 411 older adults who have all three data types." RNA sequencing data were used for the eQTL analysis in that paper. The eQTL and other -QTL identified in the paper can also be downloaded directly: http://mostafavilab.stat.ubc.ca/xQTLServe/. Dear Mette,
Thanks for your reply~I have signed the ROSMAP DUC and have the opportunity to download microarray (syn3800853) and RNA sequencing (syn3388564) data.
Yes, the ROSMAP study has generated gene expression data both through microarray (syn3800853) and RNA sequencing (syn3388564)and I have downloaded them. And I have also downloaded two batches of genotype data(syn3157325).
But what I'm confused is which expression data should I choose to make eQTL analysis with genotype data? microarray (syn3800853) or RNA sequencing (syn3388564)? or both?
And I tried to find the explanations in this paper( Bernard et al., An xQTL map integrates the genetic architecture of the human brain's transcriptome and epigenome. Nature neuroscience. 2017), however, it seems there are no interpretations.
I'm looking foward to hearing from you soon.
Thanks so much and have a nice day.
Best,
XiaoYan
The ROSMAP study has gene expression data generated both through microarray (syn3800853) and RNA sequencing (syn3388564). You do need to sign the ROSMAP DUC for data access, if you have not done this yet (a window will prompt you to how to do this once you try to download a file)
Drop files to upload
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