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. Author manuscript; available in PMC: 2022 Nov 3.
Published in final edited form as: Neuron. 2021 Sep 1;109(21):3402–3420.e9. doi: 10.1016/j.neuron.2021.08.003

KEY RESOURCES TABLE

REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies
Chick polyclonal Anti-MAP2 ABCAM Cat. # AB5392,
RRID AB_2138153
Mouse monoclonal Anti-SATB2 (C-terminal) ABCAM Cat. # AB51502
RRID AB_882455
Rabbit polyclonal Anti-Synapsin 1 Calbiochem Cat. # 574777
Rabbit polyclonal Anti-Tau (MAPT) Dako Cat. # A0024
RRID AB_10013724
Mouse monoclonal Anti-Phospho-Tau (Ser202, Thr205) (AT8) ThermoFisher Cat. # MN1020
RRID AB_223647
Rabbit monoclonal Anti-β-Tubulin III (clone 5H16) Millipore Cat. # MAB1637
RRID AB_2210524
Mouse monoclonal Anti-NeuN Millipore Cat. # MAB377
RRID AB_2298772
Rabbit monoclonal Anti-PPP1R1A (clone EP902Y) Abcam Cat. # Ab40877
RRID AB_775773
Mouse monoclonal Anti-PP1, PPP1CA (clone E-9) Santa Cruz Cat. # sc-7482
RRID AB_628177
Rabbit monoclonal anti-β-Amyloid (1-37) (D2A6H) Cell Signaling Technology Cat. # 12467S
RRID AB_2797928
Mouse monoclonal Anti-pT181 Tau (AT270) ThermoFisher Cat. # MN1050
RRID AB_223651
Rabbit polyclonal Anti-pT217 Tau GeneTex Cat. # GTX24851
RRID AB_373931
Bacterial and Virus Strains
FUdeltaGW-rtTA Zhang et al., 2013 Addgene plasmid # 19780
Tet-O-FUW-EGFP Zhang et al., 2013 Addgene plasmid # 30130
pTet-O-Ngn2-puro Zhang et al., 2013 Addgene plasmid # 52047
Biological Samples
HUMAN BRAIN SAMPLES MPFC RUSH RADC BRAIN BANK https://www.radc.rush.edu/
Chemicals, Peptides, and Recombinant Proteins
PP1 inhibitor: Tautomycin Sigma CAS 109946-35-2
iGSM Fenofibrate Santa Cruz Biotechnologies cat. # F6020
GSM PF-06442609 Pfizer cat. # PF-06442609
DNQX disodium salt, Tocris Bioscience Fisher Scientific cat. # 23-121-0
D-AP5, Tocris Bioscience Fisher Scientific cat. # 01-061
Streptavidin Sulfo-TAG Meso Scale Discovery cat. # R32AD-5
C2 Ceramide MedChemExpress cat. # HY-101180
Critical Commercial Assays
MSD V-PLEX Plus Aβ Peptide Panel 1 (6E10) Kit MesoScale Discoveries cat. # K15200G-1
MSD V-PLEX sAPPα/sAPPβ Kit MesoScale Discoveries cat. #K15120E-1
Aβx-37 ELISA Liu et al., 2021. N/A
Deposited Data
RNAseq data from human iNs This paper http://doi.org/10.7303/syn25169976
Proteomics data from human iNs This paper http://doi.org/10.7303/syn25169976
Experimental Models: Cell Lines
HUMAN IPSC LINE: BR01 This paper BR01, AJ0006
HUMAN IPSC LINE: BR04 This paper BR04, AJ0056
HUMAN IPSC LINE: BR08 This paper BR08, AJ0044
HUMAN IPSC LINE: BR09 This paper BR09, AJ0038
HUMAN IPSC LINE: BR103 This paper BR103, AJ0121
HUMAN IPSC LINE: BR104 This paper BR104, AJ0113
HUMAN IPSC LINE: BR108 This paper BR108, AJ0117
HUMAN IPSC LINE: BR11 This paper BR11, AJ0002
HUMAN IPSC LINE: BR13 This paper BR13, AJ0039
HUMAN IPSC LINE: BR14 This paper BR14, AJ0003
HUMAN IPSC LINE: BR15 This paper BR15, AJ0008
HUMAN IPSC LINE: BR21 This paper BR21, AJ0046
HUMAN IPSC LINE: BR22 This paper BR22, AJ0021
HUMAN IPSC LINE: BR24 This paper BR24, AJ0040
HUMAN IPSC LINE: BR26 This paper BR26, AJ0043
HUMAN IPSC LINE: BR27 This paper BR26, AJ0001
HUMAN IPSC LINE: BR28 This paper BR28, AJ0029
HUMAN IPSC LINE: BR29 This paper BR29, AJ0030
HUMAN IPSC LINE: BR30 This paper BR30, AJ0042
HUMAN IPSC LINE: BR33 This paper BR33, AJ0047
HUMAN IPSC LINE: BR36 This paper BR36, AJ0022
HUMAN IPSC LINE: BR37 This paper BR37, AJ0031
HUMAN IPSC LINE: BR39 This paper BR39, AJ0005
HUMAN IPSC LINE: BR40 This paper BR40, AJ0045
HUMAN IPSC LINE: BR41 This paper BR41, AJ0024
HUMAN IPSC LINE: BR43 This paper BR43, AJ0020
HUMAN IPSC LINE: BR46 This paper BR46, AJ0004
HUMAN IPSC LINE: BR48 This paper BR48, AJ0028
HUMAN IPSC LINE: BR50 This paper BR50, AJ0041
HUMAN IPSC LINE: BR54 This paper BR54, AJ0048
HUMAN IPSC LINE: BR57 This paper BR57, AJ0073
HUMAN IPSC LINE: BR58 This paper BR58, AJ0068
HUMAN IPSC LINE: BR59 This paper BR59, AJ0072
HUMAN IPSC LINE: BR60 This paper BR60, AJ0067
HUMAN IPSC LINE: BR61 This paper BR61, AJ0076
HUMAN IPSC LINE: BR62 This paper BR62, AJ0069
HUMAN IPSC LINE: BR63 This paper BR63, AJ0070
HUMAN IPSC LINE: BR64 This paper BR64, AJ0066
HUMAN IPSC LINE: BR65 This paper BR65, AJ0080
HUMAN IPSC LINE: BR66 This paper BR66, AJ0094
HUMAN IPSC LINE: BR67 This paper BR67, AJ0099
HUMAN IPSC LINE: BR68 This paper BR68, AJ0095
HUMAN IPSC LINE: BR69 This paper BR69, AJ0103
HUMAN IPSC LINE: BR72 This paper BR72, AJ0090
HUMAN IPSC LINE: BR83 This paper BR83, AJ0083
HUMAN IPSC LINE: BR89 This paper BR89, AJ0089
HUMAN IPSC LINE: BR91 This paper BR91, AJ0115
HUMAN IPSC LINE: BR92 This paper BR92, AJ0116
HUMAN IPSC LINE: BR93 This paper BR93, AJ0114
HUMAN IPSC LINE: BR95 This paper BR95, AJ0119
HUMAN IPSC LINE: BR97 This paper BR97, AJ0123
HUMAN IPSC LINE: BR98 This paper BR98, AJ0109
HUMAN IPSC LINE: BR99 This paper BR99, AJ0107
Human iPS Cell Line (Episomal, CD34+, ApoE2) Alstem cell advancement iPS46
Human iPS Cell Line (Episomal, CD34+, ApoE Knockout) Alstem cell advancement iPS36
Human iPS Cell Line (Episomal, CD34+, ApoE3) Alstem cell advancement iPS26
Human iPS Cell Line (Episomal, CD34+) Alstem cell advancement iPS16
Software and Algorithms
R Studio, v3.6.1 of R; v1.2.5019 of R Studio R Core Team, 2020 https://www.rstudio.com
pairwiseCorrSkew.R for generating Figure 3 correlations and skew This paper; zenodo https://doi.org/10.5281/zenodo.5161656
FIJI Schindelin et al., 2012 https://imagej.net/Fiji/Downloads
Kallisto pseudoalignment quantification program, v0.43.1 Bray et al., 2016. https://github.com/pachterlab/kallisto
Sleuth, v0.30.0 Pimentel et al., 2017 https://www.rdocumentation.org/packages/sleuth/versions/0.30.0
Gene Set Enrichment Analyses (GSEA) Subramanian et al., 2005 https://www.gsea-msigdb.org/gsea/index.jsp
ComBat algorithm in the SVA (v3.34.0) package in R Johnson et al., 2007 https://www.bioconductor.org/packages/release/bioc/vignettes/sva/inst/doc/sva.pdf
MaxQuant v1.6.3.4 Cox et al., 2008 https://github.com/galaxyproteomics/tools-galaxyp/
WGCNA Langfelder et al., 2008 https://cran.r-project.org/web/packages/WGCNA/index.html
TAMPOR Johnson et al., 2020 https://github.com/edammer/TAMPOR/