KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
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| Antibodies | ||
|
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| Anti-UBQLN2 1:1000 | Cell Signaling | Cat. #85509S; RRID:AB_2800056 |
| Anti-Actin 1:1000 | Abcam | Cat. #ab216070 |
|
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| Bacterial and virus strains | ||
|
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| E. Coli DH10B | Life Technologies | Cat. #18290015 |
| NEB Stable Competent E. Coli. Strain | New England Biolabs | Cat. #C3040H |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
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| Extreme Gene 9 transfection reagent | Millipore-Sigma | Cat. #6365787001 |
| GlutaMax-I | ThermoFisher | Cat. #A1286001 |
| Chloroquine | Millipore-Sigma | Cat. #C6628 |
| Bovine serum albumin | Millipore-Sigma | Cat. #A8022 |
| Sodium butyrate | Millipore-Sigma | Cat. #303410 |
| GlutaMax-supplemented OptiMem | ThermoFisher | Cat. #51–985-034 |
| Recombinant human epidermal growth factor | ConnStem | Cat. #E1000 |
| Recombinant human fibroblast growth factor | ConnStem | Cat. #F1001 |
| StemPro neural supplement | Life Technologies | Cat. #A1050801 |
| Corning Matrigel GFR membrane matrix | Fisher Scientific | Cat. #CB-40230C |
| Polybrene | Millipore-Sigma | Cat. #TR-1003-G |
|
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| Critical commercial assays | ||
|
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| Gibson assembly Master Mix | New England Biolabs | Cat. #E2611L |
| BioRad Calirty Max Western ECL Substrate, | BioRad | Cat. #175063 |
| LabForce HyBlot CL | Thomas Scientific | Cat. # 114J51 |
| Qiagen RNeasy Kit | Qiagen | Cat. #74304 |
| Invitrogen SuperScript III First Strand Synthesis SuperMix |
ThermoFisher | Cat. #18080400 |
| Endo-Free Maxi Prep Isolation Kits | Qiagen | Cat. #12362 |
| Mouse Neural Stem Cell Nucleofection Kit | Lonza | Cat. # VPG-1004 |
| SYBR Green I reagents | Roche Diagnostics | Cat. #04707516001 |
| Gibco CELLstart CTS | Thermo Fisher | Cat. #A10142–01 |
| Gibco neurobasal media | Thermo Fisher | Cat. #21103 |
| Gibco serum-free B27 | Thermo Fisher | Cat. #17504 |
|
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| Deposited data | ||
|
| ||
| Sequencing data for massively parallel sgRNA-Cas9 disruption and individual replicate disruption | This paper | GSE138823 |
| Sequencing data for RNA-seq and H3K27ac enrichment collected from H9-dervived human neural stem cells | Cotney et al.24 | GSE57369 |
| H3K27ac enrichment data in human embryonic limb | Cotney et al.40 | GSE42413 phs001226.v1.p1 |
| H3K27ac enrichment data in human embryonic cortex | Reilly et al.2 | GSE63649 phs001226.v1.p1 |
| H3K27ac data in human H1 ESCs and adult tissues profiled by the Roadmap Epigenomics Project | Kundaje et al.84 | GSE16368 |
| PsychEncode Hi-C Data from human fetal brain | Rajarajan et al.70 | syn22343893 |
| Single-cell human fetal brain RNA-sequencing data | Bhaduri et al.74 Eze et al.75 | NeMO identifier: nemo:dat-0rsydy7 |
| JASPAR 2018 database | Khan et al.65 | https://jaspar2018.genereg.net/ |
| Epilogos | https://epilogos.altius.org | N/A |
|
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| Experimental models: Cell lines | ||
|
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| H9-derived human neural stem cells | Life Technologies | Cat. #N7800–1000 |
| HEK293FT | Invitrogen | Cat. #R70007 |
| HEK293T | Yale Cell Preparation and Analysis Core | N/A |
|
| ||
| Oligonucleotides | ||
|
| ||
| Oligonucleotides used to clone sub-libraries and in validation and RT-qPCR assays are listed in Table S14. | This paper | N/A |
|
| ||
| Recombinant DNA | ||
|
| ||
| LentiCRISPRv2GFP | Addgene | Cat. #82416 |
| pCMV-VSV-G | Addgene | Cat. #8454 |
| pCMV-dR8.2 dvpr | Addgene | Cat. #8455 |
|
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| Software and algorithms | ||
|
| ||
| Bowtie v. 1.1.2 | Langmead et al.85 | https://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.2/ |
| CRISPResso2 | Clement et al.86 | http://crispresso2.pinellolab.org/submissiongreat.stanford.edu |
| GREAT version 3.0.0 | McLean et al.87 | |
| MAGeCK version 0.5.8 | Li et al.88 | https://sourceforge.net/projects/mageck/files/0.5/ |
| MASS (v7.3–54) | Venables and Ripley89 | https://www.stats.ox.ac.uk/pub/MASS4/ |
| DAVID v6.8 | Huang et al.90 Huang et al.91 |
https://david.ncifcrf.gov/ |
| ReactomePA package (v1.14.0) | Fabregat et al.61 | https://bioconductor.org/packages/release/bioc/html/ReactomePA.html |
| Seurat R package (v4.3.0) | Hao et al.92 | https://satijalab.org/seurat/ |
| Batchelor R package (v1.8.1) | Haghverdi et al.93 | https://www.bioconductor.org/packages/release/bioc/html/batchelor.html |
| ComplexHeatmap R package (v2.11.2) | Gu94 | https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| Cutadapt version 1.16 | Martin95 | https://cutadapt.readthedocs.io/en/v1.16/index.html |
| Juicer | Durand et al.96 | https://github.com/aidenlab/juicer/ |
| ShinyGO | Ge et al.80 | http://bioinformatics.sdstate.edu/go/ |
| Nebulosa v1.2.0 | Alquicira-Hernandez and Powell97 | https://www.bioconductor.org/packages/release/bioc/html/Nebulosa.html |
| ImageJ | Schneider et al.98 | https://imagej.net/ |
| Original code for analyses performed in this study | This paper | https://doi.org/10.5281/zenodo.10258136 |
|
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| Other | ||
|
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| Amicon Ultra-15 100kD filters | Millipore-Sigma | Cat. # UFC901008 |
| CustomArray 90K oligonucleotide synthesis array | CustomArray | N/A |
| Proliferation-decreasing controls, described in the Methods | Wang et al.22 | N/A |
| Accuri C6 Flow Cytometer | BD Biosciences | N/A |
| S3e Cell Sorter | BioRad | N/A |
| Cytoflex LR Flow Cytometer | Beckman Coulter | N/A |
| Roche LightCycler 480 PCR Thermal Cycler | Roche Diagnostics | N/A |
| HiSeq 4000 | Illumina | N/A |
| MiSeq | Illumina | N/A |