KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-H3K27Ac | Active Motif | Cat# 39133, RRID:AB_2561016 |
| Rabbit polyclonal anti-H3.3 | Millipore | Cat# 09-838, RRID:AB_10845793 |
| Rabbit polyclonal ant-H3K27M (ChIP-seq, dot blot) | Millipore | Cat# ABE419, RRID:AB_2728728 |
| Rabbit monoclonal anti-PPIB | Abcam | Cat# ab178397 |
| Rabbit polyclonal anti-p38 MAPK | CST | Cat# 9212S |
| Rabbit polyclonal anti-phospho-p38 MAPK | CST | Cat# 9211S |
| Rabbit polyclonal anti-H3 | Abcam | Cat# ab1791 |
| Rabbit polyclonal anti-H3K27me3 | Active Motif | Cat# 39155, RRID:AB_2561020 |
| Mouse monoclonal anti-EED | Active Motif | Cat# 61203, RRID:AB_2615071 |
| Rabbit monoclonal anti-H3K27M (Immunofluorescence) | Abcam | Cat# ab190631 |
| Mouse monoclonal anti-nestin | Abcam | Cat# ab6320, RRID:AB_308832 |
| Chicken polyclonal anti-GFP | Abcam | Cat# ab13970, RRID:AB_300798 |
| Rabbit polyclonal anti-Olig2 | Millipore | Cat# AB9610, RRID:AB_570666 |
| Goat polyclonal anti-Sox10 | R&D | Cat# AF2864 |
| Rabbit polyclonal anti-Cspg4 | Millipore | Cat# AB5320, RRID:AB_11213678 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| SB202190 | SelleckChem | Cat# S1077 |
| Human WNT3A | R&D Systems | Cat# 5036-WN-010 |
| Human WNT5A | R&D Systems | Cat# 645-WN-010 |
| SiR-actin | Cytoskeleton | Cat# cy-SC001 |
| MitoTracker Red CMXRos | Thermo | Cat# M7512 |
| Lucifer Yellow CH lithium salt | Thermo | Cat# L453 |
| SB431542 | Stemgent | Cat# 04-0010 |
| LDN193189 | Stemgent | Cat# 04-0074 |
| Retinoic acid | Sigma | Cat# R2625 |
| Smoothened agonist | Millipore | Cat# 566660 |
| Human PDGF-AA | R&D | Cat# 221-AA-050 |
| Human IGF-1 | R&D | Cat# 291-G1-200 |
| Human HGF | R&D | Cat# 294-HG-025 |
| Human NT-3 | Millipore | Cat# GF031 |
| Human T3 | Sigma-Aldrich | Cat# T2877 |
| Biotin | Sigma-Aldrich | Cat# 4639 |
| cAMP | Sigma-Aldrich | Cat# D0260 |
| Drosophila Spike-In Chromatin | Active Motif | Cat# 53083 |
| Critical Commercial Assays | ||
| SureSelectXT Human All Exon v6 | Agilent | Cat# 5190-8863 |
| Nextera Rapid Capture Exome | Illumina | Cat# 20020616 |
| NEBNext Multiplex Oligos for Illumina (Index Primers 1-12) | NEB | Cat# E7335S |
| NEBNext Multiplex Oligos for Illumina (Index Primer Set 2) | NEB | Cat# E7500Ss |
| Nextera DNA Library Prep Kit | Illumina | Cat# FC-121-1030 |
| CellTiter-Glo | Promega | Cat# G9243 |
| RhoA G-LISA Activation Assay Kit | Cytoskeleton | Cat# BK124 |
| NEBNext Ultra II DNA Library Prep Kit | NEB | Cat# E7645S |
| Deposited Data | ||
| Raw and processed data | This paper | GEO GSE126319 |
| Primary DIPG single cell RNA-seq | Filbin et al. 2018 | GEO GSE102130 |
| Primary DIPG whole tissue RNA-seq | Grasso et al. 2015 | dbGaP phs000900.v1.p1 |
| H3K27M NPC Microarray | Funato et al. 2014 | GEO GSE55541 |
| HMEC contact domain list | Rao et al. 2014 | GEO GSE63525 |
| Human hg19 reference genome NCBI build 37, GRCh37 | UCSC Genome Browser | http://hgdownload.soe.ucsc.edu/downloads.html |
| Human CpG island annotations | UCSC Genome Browser | http://hgdownload.soe.ucsc.edu/downloads.html |
| Drosophila dm6 reference genome | UCSC Genome Browser | http://hgdownload.soe.ucsc.edu/downloads.html |
| RefSeq gene annotations | UCSC Genome Browser | https://genome.ucsc.edu |
| Experimental Models: Cell Lines | ||
| Human: 2242-1 iSPC cells | Laboratory of Sergiu Pasca | N/A |
| Human: Patient-derived DIPG cultures | Laboratory of Michelle Monje | Grasso et al., 2015; Nagaraja et al., 2017; Qin et al., 2017; this paper |
| Experimental Models: Organisms/Strains | ||
| Oligonucleotides | ||
| Recombinant DNA | ||
| 7TG (7xTCF/LEF GFP) | Brugmann et al., 2007 | RRID:Addgene_24314 |
| Human HIST1H3B Gene ORF cDNA clone expression plasmid, C-HA tag (pCMV3) | Sino Biological | Cat# HG15814-CY |
| Super piggyBac Transposase expression vector | Laboratory of Joanna Wysocka | N/A |
| PiggyBac Transposase | Laboratory of Joanna Wysocka | N/A |
| Software and Algorithms | ||
| bowtie2 | Langmead et al., 2012 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| samtools | Li et al., 2009 | http://samtools.sourceforge.net/ |
| picardtools | Broad Institute, GitHub Repository | https://broadinstitute.github.io/picard/ |
| bedtools | Quinlan et al., 2010 | https://bedtools.readthedocs.io/en/latest/ |
| bedGraphToBigWig | Kent et al., 2010 | https://www.encodeproject.org/software/bedgraphtobigwig/ |
| macs2 | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| tophat2 | Kim et al., 2013 | https://ccb.jhu.edu/software/tophat/index.shtml |
| Rsubread | Liao et al., 2014 | https://bioconductor.org/packages/release/bioc/html/Rsubread.html |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| Rank Ordering of Super-Enhancers (ROSE) | Whyte et al., 2013; Loven et al., 2013 | http://younglab.wi.mit.edu/super_enhancer_code.html |
| Cytoscape Enrichment Map | Merico et al., 2010 | https://www.baderlab.org/Software/EnrichmentMap |
| BWA | Li et al., 2009 | http://bio-bwa.sourceforge.net/ |
| GATK | McKenna et al., 2010 | https://software.broadinstitute.org/gatk/ |
| FATHMM-MKL | Shihab et al., 2015 | http://fathmm.biocompute.org.uk/fathmmMKL.htm |
| VarScan 2 | Koboldt et al., 2012 | http://dkoboldt.github.io/varscan/ |
| ExomeDepth | Plagnol et al., 2012 | https://cran.r-project.org/web/packages/ExomeDepth/index.html |
| ChromVAR | Schep et al., 2017 | https://github.com/GreenleafLab/chromVAR |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| CellProfiler | McQuin et al., 2018 | https://cellprofiler.org/ |
| Other | ||