KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-ACSS2 | Cell Signaling | Cat# 3658S; RRID:AB_2222710 |
| Rabbit polyclonal anti-ACADS | ThermoFisher | Cat# PA5-54580; RRID:AB_2637583 |
| Goat polyclonal anti-SOX17 | R&D systems | Cat# AF1924-SP; RRID:AB_355060 |
| Rabbit polyclonal anti-ACOX3 | ThermoFisher | Cat# PA5-57422; RRID:AB_2637608 |
| Rabbit monoclonal anti-FOXA2 | Cell Signaling | Cat# 8186T; RRID:AB_10891055 |
| Rabbit polyclonal pan anti-crotonyllysine | PTM Biolabs | Cat# PTM-501; RRID:AB_2877694 |
| Mouse monoclonal pan anti-crotonyllysine | PTM Biolabs | Cat# PTM-502; RRID:AB_2877695 |
| Rabbit monoclonal anti-H3K27ac | Abcam | Cat# ab177178; RRID:AB_2828007 |
| Rabbit polyclonal pan anti-butyryllysine | PTM Biolabs | Cat# PTM-301; RRID:AB_2687946 |
| Rabbit polyclonal pan anti-acetyllysine | PTM Biolabs | Cat# PTM-105; RRID:AB_2877698 |
| Mouse monoclonal anti-Actin, clone C4 | Millipore | Cat# MAB1501; RRID:AB_2223041 |
| Rabbit polyclonal anti-H3 | Abcam | Cat# ab1791; RRID:AB_302613 |
| Rabbit polyclonal anti-acetylated lysine | Cell Signaling | Cat# 9441s; RRID: RRID:AB_331805 |
| Rabbit polyclonal anti-CDH17 | Sigma | Cat# HPA026556; RRID:AB_1845897 |
| Rabbit monoclonal anti-ACTN2 [EP2529Y] | Abcam | Cat# ab68167; RRID:AB_11157538 |
| Donkey anti-rabbit IgG H&L (Biotin) | Abcam | Cat# ab97062; RRID:AB_10679678 |
| Mouse monoclonal anti-Histone H3 Antibody, clone 6.6.2 | Millipore | Cat# 05-499; RRID:AB_309763 |
| Rabbit polyclonal anti-beta III tubulin | Abcam | Cat# ab18207; RRID:AB_444319 |
| Bacterial and virus strains | ||
| One shot Stbl3™ chemically competent | Thermo Fisher | Cat# C737303 |
| Chemicals, peptides, and recombinant proteins | ||
| Matrigel hESC-qualified | Corning | Cat# 354277 |
| Y-27632 dihydrochloride (ROCK inhibitor) | TOCRIS | Cat# 1254 |
| Crotonic acid | Sigma | Cat# 113018 |
| Sodium acetate | Sigma | Cat# S2889 |
| L-Arginine-13C6,15N4 hydrochloride | Sigma | Cat# 608033 |
| L-Lysine-13C6,15N2 hydrochloride | Sigma | Cat# 608041 |
| Crotonyllysine peptide library | Dr. Yingming Zhao’s lab | This paper |
| Butyrylysine peptide library | Dr. Yingming Zhao’s lab | This paper |
| Critical commercial assays | ||
| STEMDIFF trilineage differentiation kit | Stem Cell Technology, Inc. | Cat# 05230 |
| Deposited data | ||
| RNaseq data | This paper | GEO: GSE130345 |
| scRNA-seq data | This paper | GEO: GSE130341 |
| ChIP-seq data | This paper | GEO: GSE130344 |
| Unprocessed and uncompressed immuno-blots | This paper | https://doi.org/10.17632/sfpv2m95s6.1 |
| Experimental models: cell lines | ||
| Mel1 hESCs | Dr. Andrew Elefanty and Edouard Stanley at the University of Queensland, Australia | NIH Registration number: 0139 |
| H9 hESCs | Dr. James A. Thomson at University of Wisconsin-Madison (via WiCell Research Institute) | NIH Registration number: 0062; RRID:CVCL_9773 |
| ACADS KO mel1 hESCs | This paper | N/A |
| ACOX3 KO mel1 hESCs | This paper | N/A |
| Experimental models: organisms/strains | ||
| NSG CD34FL (NOD.Cg-Prkdcscid Il2rgtm1Wjl /SzJ) | Jackson Laboratory | #005557 |
| Oligonucleotides | ||
| Please see Table S7 | N/A | |
| Recombinant DNA | ||
| EF1a-cas9-nls | Stolfi et al., 2014 | Addgene plasmid #59987; RRID:Addgene_59987 |
| LentiCRISPR v2 | Sanjana et al., 2014 | Addgene plasmid #52961; RRID:Addgene_52961 |
| AAVS1_puro_PGK1_3xFLAG_Twin_Strep_EZH2 | Dalvai et al., 2015 | Addgene plasmid #79902; RRID:Addgene_79902 |
| LentiCRISPR-ACADS sgRNA | This paper | N/A |
| LentiCRISPR-ACOX3 sgRNA | This paper | N/A |
| AAVS1_puro_PGK1_H4-GFP | This paper | N/A |
| AAVS1_puro_PGK1_H4K77R-GFP | This paper | N/A |
| AAVS1_puro_PGK1_H4K91R-GFP | This paper | N/A |
| Software and algorithms | ||
| Trim Galore (version 0.4) | https://github.com/FelixKrueger/TrimGalore | |
| Microsoft Office Excel (version 16.16.27) | Microsoft | N/A |
| Bowtie | Langmead et al., 2009 | N/A |
| Samtools (version 1.3.1) | Li et al., 2009 | N/A |
| Picard (version 1.115) | http://broadinstitute.github.io/picard | |
| MultiBamSummary | N/A | |
| FindPeaks from Homer (version 4.8.3) | Heinz et al., 2010 | N/A |
| MergeBed from bedTools (version 2.25.0) | Quinlan and Hall, 2010 | N/A |
| Bioconductor package DESeq2 | Love et al., 2014 | N/A |
| GREAT (version 3.0.0) | Mclean et al., 2010 | N/A |
| Deeptools (version 2.4.2) | Ramírez et al., 2016 | N/A |
| STAR aligner (version 2.6) | Dobin et al., 2013 | N/A |
| FeatureCounts (version 1.4.6) | Liao et al., 2013 | N/A |
| Partek Genomic Suite (version 6.6) | Partek | N/A |
| UMI-tools (version 0.5.0) | Smith et al., 2017 | N/A |
| R (version 3.5.0) | https://www.r-project.org/ | |
| DropletUtils (version 1.2.2) | Griffiths et al., 2018 | N/A |
| Seurat package (version 2.3.4) | Satija et al., 2015 | N/A |
| SCENIC | Aibar et al., 2017 | N/A |
| Github | https://github.com/aertslab/SCENIC | |
| Monocle2 (version 2.10.1) | Qiu et al., 2017 | N/A |