KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-HMGCS2 antibody [EPR8642] | Abcam | Cat#ab137043: RRID:N/A |
| Anti-Vinculin antibody [EPR8185] | Abcam | Cat#ab129002: RRID:AB_11144129 |
| H3K4me3 | Abcam | Cat#ab8580: RRID:AB_306649 |
| H3K4me1 | Abcam | Cat#ab8895: RRID:AB_306847 |
| H3K9me3 | Abcam | Cat#ab8898: RRID:AB_306848 |
| H3K27ac | Abcam | Cat#ab4729: RRID:AB_2118291 |
| H3K27me3 | Abcam | Cat#ab6002: RRID:AB_305237 |
| H3K79me2 | Abcam | Cat#ab3594: RRID:AB_303937 |
| H3K9ac | Abcam | Cat#ab4441: RRID:AB_2118292 |
| H3K14ac | Millipore | Cat#07-353: RRID:AB_310545 |
| H3 | Cell Signaling | Cat#4499: RRID:AB_10544537 |
| H4 | Abcam | Cat#ab31830: RRID:AB_1209246 |
| H3K9-β-hydroxybutyryllysine | PTM Bio | Cat#PTM-1250: RRID:N/A |
| H4K12-β-hydroxybutyryllysine | PTM Bio | Cat#PTM-1206: RRID:N/A |
| Anti-rabbit IgG, horseradish peroxidase (HRP)-linked | Cell Signaling | CAT#7074S: RRID:AB_2099233 |
| Goat Anti-Rabbit IgG (H+L) Antibody, Alexa Fluor 594 Conjugated | ThermoFisher | Cat#A-11012: RRID:AB_141359 |
| Chemicals, peptides, and recombinant proteins | ||
| TGF-β RI Kinase Inhibitor VI | Calbiochem | CAT#SB431542 |
| Y-27632 dihydrochloride | Millipore Sigma | CAT#Y0503 |
| N-acetylcysteine amide | Millipore Sigma | CAT#A0737 |
| Trichostatin A (TSA), Ready Made Solution | Millipore Sigma | CAT#T1952-200UL |
| (R)-(–)-3-Hydroxybutyric acid | Millipore Sigma | CAT#298360 |
| Corning® Matrigel® Basement Membrane Matrix, *LDEV-Free, 10 mL | Corning | CAT#356234 |
| SYTOX Red | Thermo Fisher | CAT# S34859 |
| enhanced chemiluminesence (ECL) | Thermo Fisher | CAT#34080 |
| Protease Inhibitor Cocktail Set I - Calbiochem | Millipore Millipore Sigma | CAT#539131 |
| Dynabeads Protein G for Immunoprecipitation | Thermo Fisher | CAT#10004D |
| ProLong Gold Antifade Mountant with DAPI | Thermo Fisher | CAT#P36935 |
| Borg Decloaker | Biocare Medical | CAT#BD1000 |
| Solid-Phase Reversible Immobilization (SPRI) beads; Reagent, SPRIselect, 450mL | Beckman-Coulter | CAT#B23319 |
| ADMEM/F12 | Millipore Sigma | CAT#D6421 |
| Dulbecco’s Phosphate Buffered Saline (DPBS) (Ca2+- and Mg2+-free) | Millipore Sigma | CAT#D8537-500ML |
| HBSS (Ca2+- and Mg2+-free) | Thermo Fisher | CAT#88284 |
| Invitrogen UltraPure 0.5M EDTA, pH 8.0 | Thermo Fisher | CAT#15575020 |
| L-Glutamine (200 mM) | Millipore Sigma | CAT#25030081 |
| HEPES solution | Millipore Sigma | CAT#H0887-100ML |
| 50% L-WRN conditioned media | Guo et al., 2009 | N/A |
| Pierce 16% Formaldehyde (w/v), Methanol-free | Thermo Fisher | CAT#28908 |
| TrypLE Express Enzyme (1X), phenol red | Thermo Fisher | CAT#12605028 |
| Fetal Bovine Serum (FBS) – Premium Select | Atlanta Biologicals | CAT# |
| HyClone Penicillin Streptomycin 100X Solution | Fisher Scientific | CAT#SV30010 |
| Critical commercial assays | ||
| β-Hydroxyl-butyrate LiquiColor Test | StanBio | CAT#2440-058 |
| PicoPure RNA Isolation Kit | Thermo Fisher | CAT#KIT0204 |
| SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing | Clontech | CAT#634894 |
| Invitrogen PureLink RNA Mini Kit | Thermo Fisher | CAT#12183018A |
| High Sensitivity D1000 Reagents | Agilent Technologies | CAT#5067-5585 |
| Invitrogen Qubit dsDNA HS Assay Kit | Thermo Fisher | CAT#Q32851 |
| RNA Clean & Concentrator-25 | Zymo Research | CAT#R1017 |
| Invitrogen SuperScript III First-Strand Synthesis System | Thermo Fisher | CAT#18080051 |
| NEBNext® Ultra II DNA Library Prep Kit for Illumina® | New England Biolabs | CAT#E7645S |
| TruSeq DNA LT Sample Prep Kit | Illumina | CAT# FC-121-2001 and FC-121-2002 |
| Deposited data | ||
| Raw and analyzed data | This paper | PRJNA:506838 |
| Mouse reference genome (UCSC mm9) | Illumina iGenome | http://bowtie-bio.sourceforge.net/index.shtml |
| Ensemble annotated mouse genome features | Ensembl | https://genome.ucsc.edu/cgi-bin/hgTables |
| Experimental models: Cell lines | ||
| Primary small intestine spheroids of C57BL/6 mice | This paper | N/A |
| Experimental models: Organisms/strains | ||
| Mouse: B6.129P2-Lgr5tm1(cre/ERT2)Cle/J | The Jackson Laboratory | JAX:008875 |
| Mouse: C57BL/6J | The Jackson Laboratory | JAX:000664 |
| Oligonucleotides | ||
| Gapdh (Mm99999915_g1) | Life Technologies | CAT#4448484 |
| Lgr5 (Mm00438890_m1) | Life Technologies | CAT#4331182 |
| Olfm4 (Mm01320260_m1) | Life Technologies | CAT#4331182 |
| Hmgcs2 (Mm00550050_m1) | Life Technologies | CAT#4331182 |
| Bdh1 (Mm00558330_m1) | Life Technologies | CAT#4331182 |
| Ascl2 (Mm01268891_g1) | Life Technologies | CAT#4331182 |
| Primers for ChIP qRT-PCR, see Table S8 | This paper | See Table S8 |
| Software and algorithms | ||
| Paired-end RNaseq mapping: Bowtie2 (v2.2.2) | Langmead and Salzberg, 2012; Trapnell et al., 2009 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| Paired-end RNaseq mapping: Tophat2 (v2.0.14) | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| Gene-level read counts: HTseq | Anders et al., 2015 | https://htseq.readthedocs.io/en/release_0.11.1/ |
| Gene-level FPKM: Cufflinks | Trapnell et al., 2012 | http://cole-trapnell-lab.github.io/cufflinks/ |
| DEG analysis: DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Rawfastq ChIP-seq reads processing: snakemake based pipeline | https://github.com/crazyhottommy/pyflow-ChIPseq | |
| Raw ChIP read processing: FastQC | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | |
| Genome alignment: Bowtie (v1.1.2) | Langmead et al., 2009 | http://bowtie-bio.sourceforge.net/index.shtml |
| Duplicate read removal: SAMBLASTER | Faust and Hall, 2014 | https://github.com/GregoryFaust/samblaster |
| Downsampling: samtools (v1.5) | Li et al., 2009 | http://samtools.sourceforge.net/ |
| ChIP-seq library visualization: deepTools (v2.4.0) | Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/ |
| ChIP-seq peak calling: Model-based analysis of ChIP-seq (MACS) (v1.4.2) | Zhang et al., 2008 | http://liulab.dfci.harvard.edu/MACS/00README.html |
| Kbhb binding: DiffBind R package | Stark, 2011 | https://bioconductor.org/packages/release/bioc/html/DiffBind.html |
| Histone PTM site identification: Galaxy/Cistrome | Liu et al., 2011 | http://cistrome.org/ap/root |
| Gene body heatmaps and average density plots: ngs.plot | Shen et al., 2014 | https://github.com/shenlab-sinai/ngsplot |
| Chromatin state patterns: ChromHMM | Ernst and Kellis, 2012 | http://compbio.mit.edu/ChromHMM/ |
| Gene enrichment analysis: genomic regions enrichment of annotations tool (GREAT) | McLean et al., 2010 | http://great.stanford.edu/public/html/ |
| GraphPad Prism 8.0 | GraphPad Software Inc. | https://www.graphpad.com:443/scientific-software/prism/ |