Data for: Raw count data, transcribed variant count data, and reference genomic annotation files for Boocock et al. 2024

Expression quantitative trait loci (eQTLs) provide a key bridge between noncoding DNA sequence variants and organismal traits. The effects of eQTLs can differ among tissues, cell types, and cellular states, but these differences are obscured by gene expression measurements in bulk populations. We developed a one-pot approach to map eQTLs in Saccharomyces cerevisiae by single-cell RNA sequencing (scRNA-seq) and applied it to over 100,000 single cells from three crosses. We used scRNA-seq data to genotype each cell, measure gene expression, and classify the cells by cell-cycle stage. We mapped thousands of local and distant eQTLs and identified interactions between eQTL effects and cell-cycle stages. We took advantage of single-cell expression information to identify hundreds of genes with allele-specific effects on expression noise. We used cell-cycle stage classification to map 20 loci that influence cell-cycle progression. One of these loci influenced the expression of genes involved i..., , , ## Description of the data and file structure

Includes cell-cycle assignments in `cell_cycle_feb02152022.tsv` . Each row contains the cell-cycle assignment for cells analyzed in the experiment. Columns include the data set, cell barcode, cell-cycle assignment, and Seurat-based cluster assignments prior to manual cell-cycle assignment.

Additionally, output data structures from Cell Ranger and Vartrix are included in `processed.tar.gz`. When expanded, processed/.*/filtered_feature_bc_matrix/ contains for each single-cell experiment (experiments are indicated as the folder names in . * and are described in provided R code referenced below at github):

1. `barcodes.tsv` are cell barcodes used in analysis, each line indicates a cell barcode that was used for downstream analysis
2. `features.tsv.gz` are gene features used in analysis, each line indicates a transcript (systematic gene name and common gene name are provided)
3. `matrix.mtx.gz` are the UMI counts per transcript in sparse ma...