KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat monoclonal anti-Nanog (clone eBioMLC-51) | eBioscience | Cat#50-5761-82, RRID: AB_2574243 |
| Mouse monoclonal anti-Oct-3/4 (C-10) | Santa Cruz Biotechnology | Cat#sc-5279, RRID: AB_628051 |
| Goat polyclonal anti-SOX2 | R&D Systems | Cat#AF2018, RRID: AB_355110 |
| Goat polyclonal anti-LIF | R&D Systems | Cat# AB-449-NA, RRID:AB_354362 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant Mouse LIF protein | Isolated from Chinese Hamster Ovary (CHO) cell line | n/a |
| ESGRO Recombinant Mouse LIF protein | Millipore | Cat# ESG1107 |
| CHIR99021 GSK-3 inhibitor | Tocris | Cat# 4423, CAS: 252917-06-9 |
| PD0325901 MEK/ERK pathway inhibitor | STEMCELL Technologies | Cat# 72184, CAS: 391210-10-9 |
| Deposited data | ||
| RNA-Seq and ATAC-Seq | ArrayExpress (https://www.ebi.ac.uk/arrayexpress/) | E-MTAB-7730 (founder inbred strain mESC RNA-Seq); E-MTAB-7728 (DO mESC RNA-Seq); E-MTAB-8759 (DO mESC ATAC-Seq); and E-MTAB-8695 (allele swap mESC RNA-Seq) |
| DO mESC genotypes | Diversity Outbred Database (https://www.jax.org/research-and-faculty/genetic-diversity-initiative/tools-data/diversity-outbred-database) | “Embryonic stem cell lines from Diversity Outbred mice” |
| Processed ATAC-Seq and RNA-Seq datasets and code | github.com/daskelly/CellStemCell_2020_diverse_mESCs | N/A |
| Experimental Models: Cell Lines | ||
| NOD/ShiLtJ mESC lines, JAX strain# 1976 | Laboratory of Laura Reinholdt | AC576, AC595, & AC601 |
| NZO/HiltJ mESC lines, JAX strain# 2105 | Laboratory of Laura Reinholdt | AC652, AC653, & AC671 |
| PWD/PhJ mESC lines, JAX strain# 4660 | Laboratory of Laura Reinholdt | AC398, AC401 & AC403 |
| WSB/EiJ mESC lines, JAX strain# 1145 | Laboratory of Laura Reinholdt | AC627, AC635 & AC660 |
| A/J mESC lines, JAX strain# 646 | Laboratory of Laura Reinholdt | AJ13, AJ27 & AJ28 |
| 129S1/SvImJ mESC lines, JAX strain# 2448. | Laboratory of Laura Reinholdt | AC677, AC680 & AC681 |
| Mouse embryonic fibroblasts (MEFs) derived from C57/Bl6J | Laboratory of Laura Reinholdt | N/A |
| 183 Diversity Outbred mESC lines | Predictive Biology | N/A |
| 20 CC:RIX mESC lines, see table_S3 | Laboratory of Laura Reinholdt / this paper | 0104CC01, 0104CC02, 0104CC09, 0218CC02, 0218CC03, 0351CC01, 0511CC01, 0625CC01, 1041CC01, 1041CC05, 1105CC02, 1105CC03, 2506CC07, 3240CC18, 3240CC19, 4360CC03, 4360CC04, 5103CC01, 6109CC03, 6109CC05 |
| C57BL/6J mESC lines, JAX strain# 664 | Cell Biology Department of the Jackson Laboratory | B6#49, B6#139, B6#146 |
| CAST/EiJ mESC lines, JAX strain# 928 | Laboratory of Laura Reinholdt | WM077, WM078, & WM080 |
| Experimental Models: Organisms/Strains | ||
| Mouse: A/J | The Jackson Laboratory | JAX: 000646 |
| Mouse: C57BL/6J | The Jackson Laboratory | JAX: 000664 |
| Mouse: CAST/EiJ | The Jackson Laboratory | JAX: 000928 |
| Mouse: NOD/ShiLtJ | The Jackson Laboratory | JAX: 001976 |
| Mouse: NZO/HiLtJ | The Jackson Laboratory | JAX: 002105 |
| Mouse: PWD/PhJ | The Jackson Laboratory | JAX: 004660 |
| Mouse: WSB/EiJ | The Jackson Laboratory | JAX: 001145 |
| Mouse: 129S1/SvImJ | The Jackson Laboratory | JAX: 002448 |
| Mouse: J:DO | The Jackson Laboratory | JAX: 009376 |
| Mouse: CC001/UncJ | The Jackson Laboratory | JAX: 021238 |
| Mouse: CC002/UncJ | The Jackson Laboratory | JAX: 021236 |
| Mouse: CC003/UncJ | The Jackson Laboratory | JAX: 021237 |
| Mouse: CC004/TauUncJ | The Jackson Laboratory | JAX: 020944 |
| Mouse: CC005/TauUncJ | The Jackson Laboratory | JAX: 020945 |
| Mouse: CC006/TauUncJ | The Jackson Laboratory | JAX: 022869 |
| Mouse: CC010/GeniUncJ | The Jackson Laboratory | JAX: 021889 |
| Mouse: CC011/UncJ | The Jackson Laboratory | JAX: 018854 |
| Mouse: CC018/UncJ | The Jackson Laboratory | JAX: 021890 |
| Mouse: CC025/GeniUncJ | The Jackson Laboratory | JAX: 018857 |
| Mouse: CC032/GeniUncJ | The Jackson Laboratory | JAX: 020946 |
| Mouse: CC040/TauUncJ | The Jackson Laboratory | JAX: 023831 |
| Mouse: CC041/TauUncJ | The Jackson Laboratory | JAX: 021893 |
| Mouse: CC043/GeniUncJ | The Jackson Laboratory | JAX: 023828 |
| Mouse: CC051/TauUncJ | The Jackson Laboratory | JAX: 021897 |
| Mouse: CC060/UncJ | The Jackson Laboratory | JAX: 026467 |
| Mouse: CC061/GeniUncJ | The Jackson Laboratory | JAX: 023826 |
| Oligonucleotides | ||
| Primers for allele swap genome engineering, luciferase reporter, quantitative RTPCR, and Nr5a2 ChIP qPCR see table_S4 | this paper | N/A |
| Nanog guide sequence: CCACTTTATACTCTGAATGC | Yang et al., 2013 | N/A |
| Recombinant DNA | ||
| Nanog-2A-mCherry | Yang et al., 2013 | Addgene# 48680 |
| pSpCas9(BB)-2A-Puro (PX459) V2.0 | Ran et al., 2013. | Addgene# 62988 |
| Software and Algorithms | ||
| argyle | Morgan 2015 | 10.1534/g3.115.023739 |
| bedtools v2.26.0 | Quinlan and Hall 2010 | 10.1093/bioinformatics/btq033 |
| bowtie | Langmead et al., 2009 | 10.1186/gb-2009-10-3-r25 |
| bwa v0.7.9a | Li and Durbin 2009 | 10.1093/bioinformatics/btp324 |
| ComBat | Leek et al., 2012 | 10.1093/bioinformatics/bts034 |
| DESeq2 | Love et al., 2014 | 10.1186/s13059-014-0550-8 |
| DOQTL | Gatti et al., 2014 | 10.1534/g3.114.013748 |
| edgeR | Robinson et al., 2010 | 10.1093/bioinformatics/btp616 |
| EMASE | Raghupathy et al., 2018 | 10.1093/bioinformatics/bty078 |
| g2gtools v0.1.31 | https://github.com/churchill-lab/g2gtools | N/A |
| GBRS v0.1.6 | https://github.com/churchill-lab/gbrs | N/A |
| intermediate | https://github.com/simecek/intermediate | N/A |
| MACS v1.4.2 | Zhang et al., 2008 | 10.1186/gb-2008-9-9-r137 |
| PANTHER | Mi et al., 2017 | 10.1093/nar/gkw1138 |
| qtl2 | Broman et al., 2018 | 10.1101/414748 |
| rtracklayer | Lawrence et al., 2009 | 10.1093/bioinformatics/btp328 |
| Trimmomatic v0.33 | Bolger et al., 2014 | 10.1093/bioinformatics/btu170 |
| Processed ATAC-Seq and RNA-Seq datasets and code | github.com/daskelly/CellStemCell_2020_diverse_mESCs | N/A |