Single-Cell Sequencing Reveals Lineage-Specific Dynamic Genetic Regulation of Gene Expression During Human Cardiomyocyte Differentiation
Reem Elorbany, Joshua M Popp, Katherine Rhodes, Benjamin J Strober, Kenneth Barr, Guanghao Qi, Yoav Gilad, and Alexis Battle
A workflowr project.
Preprint available online at bioRxiv
- Quality control filtering of single cell data is done at
code/create_seurat.R
- The (cells x genes) matrix of UMI counts produced by this file is available online at GEO Series GSE175634 as a .mtx file (
GSE175634_cell_counts.mtx.gz
, cell and gene indices atGSE175634_cell_indices.tsv.gz
andGSE175634_gene_indices.tsv.gz
respectively)
- The (cells x genes) matrix of UMI counts produced by this file is available online at GEO Series GSE175634 as a .mtx file (
- Normalization of the single cell counts data is done at
code/normalize_seurat.R
- The (cells x genes) matrix of corrected UMI counts produced by this file is available as a .mtx file (
GSE175634_cell_counts_sctransform.mtx.gz
, same cell and gene indices as the uncorrected counts) - The (cells x highly variable genes) matrix of pearson residuals produced by this file is available as a .tsv file (
GSE175634_pearson_residuals_sctransform.mtx.gz
)
- The (cells x genes) matrix of corrected UMI counts produced by this file is available as a .mtx file (
- Trajectory inference is performed at
analysis/ti.ipynb
- Pseudobulk aggregation, normalization, and computation of PC covariates for both pseudobulk and bulk data are done at
code/preprocessing.R
) - Dynamic eQTL calling is done at
code/eqtl_dynamic.R
for linear eQTLs,code/eqtl_dynamic_nonlinear.R
for nonlinear dynamic eQTLs, and multiple testing correction is done atcode/mtc_dynamic.R
for linear eQTLs,code/mtc_dynamic_ttest.R
for nonlinear dynamic eQTLs
- Cell type interaction eQTL calling is performed at
code/eqtl_interaction.R
, with multiple testing atcode/mtc_interaction.R
- Overlap of dynamic eQTLs with GWAS hits is done at
code/gwas.R