This web page accompanies the manuscript titled
'Single-cell RNA sequencing identifies cell type-specific cis-eQTLs and co-expression QTLs.
', by van der Wijst et al, published in Nature Genetics.
For further questions, contact the corresponding author: lude@ludesign.nl
Study
Single cell transcriptomics of PBMCs of 47 donors from the Lifelines Deep cohort (general population, Northern part of the Netherlands). Cells of five or six different donors were pooled together in one sample pool, resulting in eight different sample pools. In total, 28.855 cells were captured and their transcriptomes were sequenced to an average depth of 74k. Genotype data is available for each donor, which allowed us to use the Demuxlet method that uses variable SNPs between the pooled individuals to determine which cell belongs to which individual. Since genotype information is lacking of 2 individuals, the transcriptome of only 45 individuals could be retrieved.
Code availability 
External tools:-
Seurat: https://github.com/satijalab/seurat
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Demuxlet: https://github.com/statgen/demuxlet
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MAGIC: https://github.com/pkathail/magic
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In-house eQTL pipeline: https://github.com/molgenis/systemsgenetics/tree/master/eqtl-mapping-pipeline
- Custom code for analyses: https://github.com/molgenis/scRNA-seq
Funding
Morris Swertz and Lude Franke are supported by grants from the Dutch Research Council (ZonMW-VIDI 917.164.455 to M.S. and ZonMW-VIDI 917.14.374 to L.F.) and L.F. is supported by an ERC Starting Grant, grant agreement 637640 (ImmRisk). The Biobank-Based Integrative Omics Studies (BIOS) Consortium is funded by BBMRI-NL, a research infrastructure financed by the Dutch government (NWO 184.021.007).
