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. Author manuscript; available in PMC: 2019 Jan 24.
Published in final edited form as: Cell Stem Cell. 2018 May 3;22(5):684–697.e9. doi: 10.1016/j.stem.2018.04.009

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