KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-Calbindin | Swant | Cat#CB38 |
| Rabbit polyclonal anti-Elavl2 | Genetex | Cat# GTX12030 |
| Rabbit polyclonal anti-Elavl2+4 | Abcam | Cat#ab72603, RRID:AB_1523538 |
| Goat polyclonal anti-GFP | Abcam | Cat#ab6658 |
| Goat polyclonal anti-Grik4 (KA1) | Santa Cruz biotechnology | Cat#sc-8917 |
| Rabbit polyclonal anti-GABA | Sigma Aldrich | Cat#a2052 |
| Rabbit polyclonal anti-Lhx9 | Thermo Fisher scientific | Cat#PA5-52675 |
| Chicken polyclonal anti-MAP2 | Abcam | Cat#ab5392, RRID:AB_2138153 |
| Mouse monoclonal anti-Nestin | Millipore | Cat# MAB5326 |
| Mouse monoclonal anti-NueN | EMD Millipore | Cat#MAB377 |
| Rabbit polyclonal anti-OXT1+ OTX2 | Abcam | Cat#ab21990 |
| Rabbit monoclonal anti- PRKCD | Abcam | Cat#182126 |
| Rabbit polyclonal anti-SCGN | Thermo Fisher scientific | Cat# PA5-30393, RRID:AB_2547867 |
| Rabbit polyclonal anti-Ctip2 | Abcam | Cat# ab18465, RRID:AB_2064130 |
| Rabbit polyclonal anti-Vglut1 | Synaptic system | Cat#135303 |
| Bacterial and Virus Strains | ||
| Lentivirus vector pBOB-synP-HTB | Addgene plasmid | Cat#30195 |
| Biological Samples | ||
| Human postmortem brain samples | Shiley-Marcos Alzheimer’s Disease Research Center brain bank (ADRC) at UCSD San Diego County Medical Examiner’s Office | http://adrc.ucsd.edu |
| Human Genomic DNA | Promega | G1471 |
| 293T cells | ATCC | 293T (ATCC) CRL-3216 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Accutase | StemCell Technologies | Cat#07920 |
| BDNF | Peprotech | Cat#450-02 |
| BDNF | R&D systems | Cat#248-BD |
| B-27 supplement | Thermo Fisher scientific | Cat#12587010 |
| Collagenase IV | Thermo Fisher scientific | Cat#17104019 |
| Cyclopamine | LC Laboratories | Cat#C-8700 |
| Dibutyryl-cAMP | Tocris | Cat#1141 |
| DAPI | Thermo Fisher Scientific | D1306, RRID:AB_2629482 |
| DKK1 | Humanzyme | Cat# HZ-7133 |
| Dibutyryl-cAMP | Tocris | Cat#1141 |
| Durcupan ACM single component A, M epoxy resin | Sigma-Aldrich | Cat#44611 |
| FGF2 | Joint protein central | Cat#1614 |
| FGF2 | Stemgent | Cat#03-0002 |
| Ketamine | Putney | |
| Laminin Mouse Protein, Natural | Thermo Fisher scientific | Cat#23017015 |
| L-ascorbic acid | Sigma-Aldrich | Cat#A4403 |
| Matrigel | Trevigen | Cat#3432-005-01 |
| Noggin | Humanzyme | Cat#HZ-1085 |
| Noggin | Peprotech | Cat#120-10C |
| N-2 supplement | Thermo Fisher scientific | Cat#17502048 |
| Picrotoxin | Millipore | Cat# 528105 |
| poly-L-lysine mol wt 70,000–150,000 | Sigma-Aldrich | Cat# P1274 |
| Poly-L-ornithine | Sigma-Aldrich | Cat# P3655 |
| Rock inhibitor | StemCell Technologies | Cat# 72308 Y-27632 |
| SB431542 | StemRD | Cat#SB-050 |
| SB431542 | Tocris | |
| WNT3a | R&D Systems | Cat#5036 |
| Xylazine | Anased, Lloyd | sc-362950Rx |
| Critical Commercial Assays | ||
| Agilent DNA 1000 Kit | Agilent | N/A |
| Phusion High-Fidelity DNA Polymerase | New England Biolabs | Cat#M0530S |
| Power SYBR Green PCR Master Mix | Thermo Fisher scientific | Cat#4368708 |
| SureCell WTA 3′ Library Prep Kit for the ddSEQ System | Illumina | Cat#20014280 |
| The High Capacity cDNA Reverse Transcription Kit | Thermo Fisher scientific | Cat#4368814 |
| TruSeq Stranded Total RNA Library Prep kit | Illumina | Cat#20020597 |
| Experimental Models: Cell Lines | ||
| GM01792 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM01835 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM02038 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM02497 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM02937 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM03651 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| GM04506 | Coriell Institute for Medical Research collection | Brennand et al., 2011 |
| Hues6 hESC line (NIH approval number NIHhESC-09-0019) | HSCI | hES Cell Line: HUES-6 |
| WT33 | Marchetto et al., 2010 | Agilent |
| 293T human embryonic kidney cells | ATCC | CRL-3216 |
| Experimental Models: Organisms/Strains | ||
| NOD-SCID mice (NOD.CB17-Prkdcscid/NCrHsd) | Envigo | N/A |
| C57BL/6NHsd | Envigo | N/A |
| Oligonucleotides | ||
| Forward primer for Elavl2 5′-CTTTGGGAGCATTGGTGAAA-3′ |
This paper | N/A |
| Reverse primer for Elavl2 3′-TTCTCTGCATCCTTGGGGT-5′ |
This paper | N/A |
| Forward primer for Dkk3 5′- TCACATCTGTGGGAGACGAA-3′ |
This paper | N/A |
| Reverse primer for Dkk3 3′-GCTGGCAGGTGTACTGGAAG-5′ |
This paper | N/A |
| Forward primer for Pvrl3 5′-GCAAAGCTGTTACATTCCCG-3′ |
This paper | N/A |
| Reverse primer for Pvrl3 3′-CAGGCTCACAGTGGGTTCA-5′ |
This paper | N/A |
| Forward primer for Pvrl3 5′- CAAAGCTGTTACATTCCCGC-3′ |
This paper | N/A |
| Reverse primer for Pvrl3 3′-CAGGCTCACAGTGGGTTCA-5′ |
This paper | N/A |
| Forward primers for Gapdh 5′- TGCACCACCAACTGCTTAGC-3′ |
This paper | N/A |
| Reverse primer for Gapdh 3′- GGCATGGACTGTGGTCATGAG-5′ |
This paper | N/A |
| Recombinant DNA | ||
| ELAVL2-EGFP (based on pCSC-GFP) | This paper | N/A |
| GRIK4-GFP (based on pCSC-EGFP) | This paper | N/A |
| pCSC-GRIK4-LL-HTB (based on vector pBOB-synP-HTB) | This paper | N/A |
| pBOB-synP-HTB | Addgene plasmid | Cat#30195 |
| PROX1-EGFP | Yu et al., 2014 | N/A |
| PROX1-5-EGFP | This paper | N/A |
| Deposited data | ||
| Raw and analyzed RNA-seq data | This paper | GEO: GSE111979 |
| Software and Algorithms | ||
| Axion’s Integrated Studio (AxIS) software (Neural activity) | Axion Biosystems | https://www.axionbiosystems.com/products/axis-software |
| Clampfit 9.0 | Molecular Devices | N/A |
| pClamp 9 software | Molecular Devices | https://www.moleculardevices.com/systems/axon-conventional-patch-clamp/pclamp-11-software-suite |
| Cutadapt (v.1.3) | Python Software Foundation | https://pypi.python.org/pypi/cutadapt |
| DESeq (v.1.16.0) | Bioconductor | https://bioconductor.org/packages/release/bioc/html/DESeq.html |
| HiSeq 2500 control software (HiSeq 2500 Sequencing System) | Illumina | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html |
| HOMER | Heinz et al., 2010 | http://homer.ucsd.edu/homer/ |
| HTSeq-count (v.0.5.4) | Anders et al., 2015 | http://htseq.readthedocs.io/en/release_0.9.1/ |
| ImageJ | NIH | https://imagej.nih.gov/ij/ |
| MATLAB | MathWorks | https://www.mathworks.com/products/matlab.html |
| NeuralMetric Tool | Axion Biosystems | Axion Biosystems |
| Neurolucida Explorer | MBF Bioscience | http://www.microlucida.com/neurolucida |
| Real-Time Analysis software (HiSeq 2500 Sequencing System) | Illumina | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html |
| SDS Software v 2.3 for 7900HT real-time PCR system | Thermo Fisher scientific | https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/applied-biosystems-7900ht-fast-real-timespcr-system.html |
| Sequencing Analysis Viewer software (HiSeq 2500 Sequencing System) | Illumina | https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html |
| STAR aligner (v.2.3.1o) | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| ZEN Imaging Software | Carl Zeiss | https://www.zeiss.com/microscopy/int/products/microscope-software/zen.html |
| Other | ||
| DMEM/F12 Glutamax | Thermo Fisher scientific | Cat#10565018 |
| mTeSR1 | StemCell Technologies | Cat#85850 |
| Microfluidic devices | Kim et al., 2012 | N/A |