Supplemental data repository for Skelly et al (2020) Cell Stem Cell: "Mapping the effects of genetic variation on chromatin state and gene expression reveals loci that control ground state pluripotency".

# Genomics of Diversity Outbred mouse embryonic stem cells

Notes:

- Any lines starting with `#` in these files are comments
- Example code for analyses presented in the paper is available at https://github.com/daskelly/CellStemCell_2020_diverse_mESCs

The files in this directory are:

* CCRIX_qPCR.tsv - data supporting top panel of Figure S3
* CCRIX_self_renewal.tsv - data supporting Figure 3E
* Nr5a2_ChIP.txt - data supporting Figure 4H
* counts_atac_norm_DO.tsv.gz - TMM-normalized counts for ATAC-Seq peaks called in Diversity Outbred samples
* counts_rna_norm_DO.tsv.gz - upper quartile-normalized counts for RNA-Seq gene expression in Diversity Outbred samples
* founder_nanog_flowcytometry.tsv.gz - data supporting Figure 1D
* genotype_probs.Rds - genotype probabilities used for QTL mapping. Format is 3D array (dimensions are samples x founder haplotypes x pseudomarkers)
* lifr_flowcytometry.tsv.gz - data supporting Figure S4C
* luciferase_assay_results.txt - data supporting Figure 4C,I
* quantitative_microscopy.tsv - data supporting Figure S1
* rna_seq_counts_allele_swap_ESCs.tsv - un-normalized estimated read counts derived from RNA-Seq data processed using EMASE as described in Methods
* rna_seq_counts_founder_ESCs.tsv - un-normalized estimated read counts derived from RNA-Seq data processed using EMASE as described in Methods