Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| H3K27ac | Abcam | ab4729 |
| H3K27ac | active motif | 91193 |
| Critical commercial assays | ||
| Arima-HiC+ kit | Arima | A101020 |
| TruSeq stranded total RNA kit | Illumina | 20020596 |
| KAPA Hyper prep kit | KAPA Biosystems | KK8500 |
| Swift Accel-NGS 2S Plus DNA Library Kit | Swift Biosciences | 21024 |
| Deposited data | ||
| H3K27ac HiChIP, H3K27ac ChIP-seq, ATAC-seq, RNA-seq, and scRNA-seq from this study | This study | SuperSeries GSE262089 |
| Published wt GSC scRNA-seq: 320, 728, 810, 1206 | Pine et al.12 | PRJNA595375 |
| Published GSC and NSC H3K27ac ChIP-seq | Mack et al.43 | GSE119776 |
| H3K27ac HiChIP: T-47D an Ishikawa cell lines | Ginley-Hidinger et al.146 | GSE227242 |
| H3K27ac HiChIP: MDA-MB-453 and MCF cell lines | Watt et al.147 | GSE157381 |
| H3K27ac HiChIP: ARK1 cell line | O’Mara et al.148 | GSE137936 |
| H3K27ac HiChIP: A673 cell line | Surdez et al.149 | GSE133227 |
| H3K27ac HiChIP: TC71 cell line | Surdez et al.149 | GSE133228 |
| H3K27ac HiChIP: WM-266–4 and COLO829 cell lines | Donohue et al.150 | GSE188401 |
| H3K27ac HiChIP: M14 cell line | Chu et al.151 | GSE156772 |
| H3K27ac HiChIP: NCI-H889 cell line | Pongor et al.152 | GSE206351 |
| H3K27ac HiChIP: NCI-H524 cell line | Pongor et al.152 | GSE206352 |
| H3K27ac HiChIP: 3 patient-derived HCC tumors | Jeon et al.153 | GSE212055 |
| H3K27ac HiChIP TCGA dataset | Yost et al.55 | https://www.cancer.gov/tcga |
| Published GDC dataset | Grossman et al.145 | https://portal.gdc.cancer.gov/ |
| Experimental models: Cell lines | ||
| Patient-Derived Glioma Stem Cells: 320, 728, 810, 1206 | National Institutes of Health and Weill Cornell Medicine/NYU Presbyterian Hospital | N/A |
| NIH-registered human H1 (WA01) embryonic stem cells | WiCell Research Institute | Cat# WA01; RRID: CVCL_9771 |
| NIH-registered human H9 (WA09) embryonic stem cells | WiCell Research Institute | Cat# WA09; RRID: CVCL_9773 |
| Oligonucleotides | ||
| For CRISPRi guide RNA sequences and RT-qPCR primer sequences, see Table S8 | ||
| Recombinant DNA | ||
| psPAX2 | N/A | Addgene #12260 |
| VSV-G | N/A | Addgene # 1488 |
| pLenti CMV rtTA3 Blast | N/A | Addgene# 26429 |
| TRE-KRAB-dCas9-IRES-GFP | Fulco et al.123 | Addgene# 85556 |
| pLKO5.GRNA.EFS.PAC vector | Heckl et al.124 | Addgene #57825 |
| Software and algorithms | ||
| TopHat2 (version 2.11) | Trapnell et al.129 | https://github.com/DaehwanKimLab/tophat2 |
| Samtools | Li et al.130 | https://github.com/samtools/ |
| htseq-count | Anders et al.131 | https://github.com/htseq |
| DESeq2 | Anders et al.132 | https://github.com/thelovelab/DESeq2 |
| bowtie2 (version 2.3.4.1) | Langmead et al.133 | https://github.com/BenLangmead/bowtie2 |
| Bedtools | Quinlan et al.134 | https://github.com/arq5x/bedtools2 |
| MACS2 | Zhang et al.135 | https://github.com/macs3-project/MACS |
| HiC-Pro pipeline (version 3.0.0) | Servant et al.136 | https://github.com/nservant/HiC-Pro |
| Juicer-tools | Durand et al.137 | https://github.com/aidenlab/JuicerTools |
| FitHiChIP (release 9.0) | Bhattacharyya et al.50 | https://github.com/ay-lab/FitHiChIP |
| Cell Ranger 2.0.1 pipeline | 10X Genomics | https://github.com/10XGenomics/cellranger |
| Seurat v4.0 | Stuart et al.78 | https://github.com/satijalab/seurat |
| ALRA | Linderman et al.138 | https://github.com/KlugerLab/ALRA |
| DoubletFinder (version 2.0.3) | McGinnis et al.139 | https://github.com/chris-mcginnisucsf/DoubletFinder |
| Nebulosa (version 1.8.0) | Leinonen et al.144 | https://github.com/powellgenomicslab/Nebulosa |
| EnrichR | Chen et al.141 | https://github.com/wjawaid/enrichR |
| LOLA | Sheffield et al.142 | https://github.com/nsheff/LOLA |
| scran | Lun et al.154 | https://github.com/elswob/SCRAN |
| umap | McInnes et al.155 | https://github.com/tkonopka/umap |
| bluster | Lun et al.156 | https://www.bioconductor.org/packages/release/bioc/html/bluster.html |
| igraph | Csardi et al.157 | https://igraph.org |
| HOMER | Heinz et al.158 | http://homer.ucsd.edu/homer/motif/ |
| Extreme limiting dilution analysis software | Hu et al.126 | http://bioinf.wehi.edu.au/software/elda |
| Other | ||